Polypeptide and immune modulation

ABSTRACT

The present invention relates to Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell, including bacteria, comprising said vector, and/or a host cell, including bacteria, comprising said polynucleotide sequence, for use in modulating the inflammation of a tissue or an organ in a subject.

CROSS-REFERENCE

This application is a division of U.S. application Ser. No. 15/704,245, filed Sep. 14, 2017, which is divisional of U.S. application Ser. No. 14/249,710, filed Apr. 10, 2014, now U.S. Pat. No. 9,796,762, issued Oct. 24, 2017, which claims the benefit of Great Britain Application No. 1306536.2, filed Apr. 10, 2013, all of which are hereby incorporated by reference in their entirety.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ANSI format and is hereby incorporated by reference in its entirety. Said ANSI copy is named “56708_702_301_SL” created Jun. 8, 2020 and is 36,864 bytes in size.

FIELD OF THE INVENTION

The present invention relates to Roseburia flagellins, and/or polynucleotide sequences encoding said Roseburia flagellins, and/or vectors comprising said polynucleotide sequences, and/or host cells, including bacteria, comprising said vectors, and/or host cells, including bacteria, comprising said polynucleotide sequences, for various therapeutic and nutritional uses.

BACKGROUND

The human intestine is thought to be sterile in utero, but is exposed to a large variety of maternal and environmental microbes immediately after birth. Thereafter, a dynamic period of microbial colonization and succession occurs which is influenced by factors such as delivery mode, environment, diet and host genotype, all of which impact upon the composition of the gut microbiota, particularly during early life. Subsequently, the microbiota stabilizes and becomes adult-like (Spor, Koren & Ley 2011). The human gut microbiota contains more than 500-1000 different phylotypes belonging essentially to two major bacterial divisions, the Bacteroidetes and the Firmicutes (Eckburg et al. 2005). The successful symbiotic relationships arising from bacterial colonization of the human gut have yielded a wide variety of metabolic, structural, protective and other beneficial functions. The enhanced metabolic activities of the colonized gut ensure that otherwise indigestible dietary components are degraded with release of byproducts providing an important nutrient source for the host. Similarly, the immunological importance of the gut microbiota is well-recognized and is exemplified in germfree animals which have an impaired immune system that is functionally reconstituted following the introduction of commensal bacteria (Macpherson et al. 2001, Macpherson, Martinic & Harris 2002, Mazmanian et al. 2005).

In sharp contrast to the production of secretory intestinal IgA, which is influenced by microbial colonization per se (Chung, Kasper 2010, Macpherson 2006), T cell development and differentiation seem to require colonization by specific commensal micro-organisms. Clostridium species, and in particular the spore-forming segmented filamentous bacteria (SFB), appear to be a potent stimulus for the differentiation and maturation of intestinal and colonic Th1, Th17 and Tregs (Gaboriau-Routhiau et al. 2009, Ivanov et al. 2009). Recent studies have now demonstrated that other gut bacteria, including those of Clostridium clusters IV and XIVa and the Altered Schaedler Flora (ASF), can induce de novo generation of Tregs while mono-colonization with Bacteroides fragilis can correct the Th1/Th2 imbalance in germfree mice by promoting the expansion of Tregs (Mazmanian et al. 2005, Geuking et al. 2011, Atarashi et al. 2011). These data infer important immune-regulatory effects of other resident gut bacteria. Clearly, the effects of commensal bacteria on T cell differentiation pathways is variable and as postulated previously may be influenced by the array of TLR ligands found associated with specific bacteria (Nutsch, Hsieh 2012). For example, the mechanism by which SFB influences T cell responses is currently unknown, but recent genome studies confirming the presence of flagellin genes suggest that innate responses mediated through TLR5-flagellin interactions may be important (Prakash et al. 2011, Sczesnak et al. 2011). Furthermore, the Treg-enhancing effects of B. fragilis have been linked with PSA and mediation by TLR2 signalling events (Round et al. 2011).

Dramatic changes in microbiota composition have been documented in gastrointestinal disorders such as inflammatory bowel disease (IBD). For example, the levels of Clostridium cluster XIVa bacteria are reduced in IBD patients whilst numbers of E. coli are increased, suggesting a shift in the balance of symbionts and pathobionts within the gut (Frank et al. 2007, Scanlan et al. 2006, Kang et al. 2010, Machiels K. et al. 2013). Interestingly, this microbial dysbiosis is also associated with imbalances in T effector cell populations.

Roseburia belongs to the phylogenetic cluster XIVa of the Firmicutes phylum. Currently, within the Roseburia genus, five species have been identified and characterised: Roseburia cecicola, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, Roseburia inuhnivorans (Stanton and Savage 1983, Duncan et al 2006). The bacteria are flagellated commensal anaerobes and are also major butyrate producers (Duncan et al. 2006). Although precise numbers of these bacteria colonizing the human gut have not been accurately estimated, Roseburia spp. are dominant in the healthy human gut and are under-represented in IBD patients (Machiels K. et al. 2013).

The roles of bacterial genes, in particular flagellin, participating in colonization and adaptation to the murine gut, as well as the host immune genes responding to colonization by Roseburia bacteria are disclosed. The inventors show that specific flagellin structures of Roseburia such as R. hominis and R. intestinalis induce distinct signalling responses in both epithelial cells and dendritic cells relative to other flagellate enteric bacteria. The importance of the TLR5-Roseburia, such as TLR5-R. hominis, interactions in directing the host adaptive response, in particular Treg responses is demonstrated. The complete genome sequence and annotation for R. hominis described herein is shown in GenBank under accession number CP003040 (version 1). For R. intestinalis (GenBank Accession Number for 16S rRNA gene strain L1-82: AJ312385) described herein the reference genome sequence is shown in GenBank under accession number ABYJ02000000 (version 2) and consists of sequences ABYJ02000001-ABYJ02000409.

STATEMENTS OF INVENTION

Surprisingly, the present inventors found that Roseburia flagellin proteins are important in modulating the immune response.

In addition, the present inventors surprisingly found that the flagellin proteins derived or derivable from Roseburia hominis or Roseburia intestinalis are important in modulating the immune response.

The present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in modulating the inflammation of a tissue or an organ (such as the intestine) in a subject.

In another aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in modulating the production of T cells (e.g. regulatory T cells such as regulatory T cells capable of expressing TLR5) in a subject.

The present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in restoring immunological tolerance.

In a further aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating the immune system of a subject.

In another aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in treating a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder.

The present invention, in another aspect, relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in modulating dendritic cells (such as bone marrow dendritic cells) and/or epithelial cells in a tissue or an organ of a subject.

The present invention, in a further aspect, relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating the production of IL-10 and/or TGFβ in a cell or cells of a subject.

In a further aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating the production of cell surface markers involved in immune responses and antigen recognition such as CD40, I-A/I-E, CD317/BST-2, CD103, CD80, CD86, CD83 and/or Siglec-H and/or the species equivalent in a cell or cells of a subject.

In another aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating (e.g. downregulating) the expression of one of more Type I IFN genes (such as but not limited to one or more genes selected from the group consisting of IFN-β1, IFN-β2, Ifi202b, Ifi203, IFI44, IFTI, MXI, OASI, OAS2, OAS3, OASL, Irf3 and Irf4) in a cell or cells of a subject.

The present invention, in a further aspect, relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating (e.g. downregulating) the expression of one or more pro-inflammatory genes (such as one or more genes selected from the group consisting of but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α) in a cell or cells of a subject.

The present invention, in another aspect, relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in improving intestinal microbiota in a subject.

In another aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating appetite in a subject.

In a further aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating (e.g. downregulating) the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject.

The present invention, in a further aspect, relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in improving alimentary canal health in a subject.

The present invention, in another aspect, relates to a pharmaceutical composition comprising a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and a pharmaceutically acceptable excipient, carrier or diluent.

In another aspect, the present invention relates to a nutritional supplement comprising a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and a nutritional acceptable excipient, carrier or diluent.

In a further aspect, the present invention relates to a feedstuff, food product, dietary supplement, or food additive comprising a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis).

The present invention, in a further aspect, relates to a process for producing a pharmaceutical composition according to the present invention, said process comprising admixing a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), with a pharmaceutically acceptable excipient, carrier or diluent; optionally said Roseburia flagellin, and/or said polynucleotide sequence, and/or said vector, and/or said host cell comprising said vector, and/or said host cell comprising said polynucleotide sequence, and/or said Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is encapsulated.

In a further aspect, the present invention relates to a process for producing a nutritional supplement according to the present invention, said process comprising admixing a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), with a nutritionally acceptable excipient, carrier or diluent; optionally said Roseburia flagellin, and/or said polynucleotide sequence, and/or said vector, and/or said host cell comprising said vector, and/or said host cell comprising said polynucleotide sequence, and/or said Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is encapsulated.

In another aspect, the present invention relates to a method of modulating the inflammation of a tissue or an organ (such as the intestine) in a subject, said method comprising administering to the subject a Roseburia flagellin, or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the inflammation of the tissue or organ (such as the intestine) in the subject is modulated.

The present invention, in another aspect, relates to a method of modulating the production of T cells (e.g. regulatory T cells such as regulatory T cells capable of expressing TLR5) in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the production of T cells (e.g. regulatory T cells such as regulatory T cells capable of expressing TLR5) in the subject is modulated.

The present invention, in a further aspect, relates to a method of regulating the immune system of a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the immune system of the subject is regulated.

In a further aspect, the present invention relates to a method of treating a disorder in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), wherein said disorder is an inflammatory disorder and/or an autoimmune disorder.

In another aspect, the present invention relates to a method of modulating dendritic cells (such as bone marrow dendritic cells) and/or epithelial cells in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein dendritic cells (such as bone marrow dendritic cells) and/or epithelial cells in the subject are modulated.

In a further aspect, the present invention relates to a method of regulating the production of IL-10 and/or TGFβ in a cell or cells of a subject, said method comprising administering a Roseburia flagellin and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), to the subject, and wherein the production of IL-10 and/or TGFβ in a cell or cells of the subject is regulated.

The present invention, in another aspect, relates to a method of regulating the production of cell surface markers involved in immune responses and antigen recognition such as CD40, I-A/I-E, CD317/BST-2, CD103, CD80, CD86, CD83 and/or Siglec-H and/or the species equivalent in a cell or cells of a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), to the subject, and wherein the production of cell surface markers involved in immune responses and antigen recognition such as CD40, I-A/I-E, CD317/BST-2, CD103, CD80, CD86, CD83 and/or Siglec-H and/or the species equivalent in a cell or cells of the subject is regulated.

In another aspect, the present invention relates to a method of regulating (e.g. downregulating) the expression of one of more Type I IFN genes (such as one or more genes selected from the group consisting of but not limited to IFN-β1, IFN-β3, Ifi202b, Ifi203, IFI44, IFTI, MXI, OASI, OAS2, OAS3, OASL, Irf3 and Irf4) in a cell or cells of a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), wherein the expression of one of more Type I IFN genes (such as one or more genes selected from the group consisting of but not limited to IFN-β1, IFN-β3, Ifi202b, Ifi203, IFI44, IFTI, MXI, OASI, OAS2, OAS3, OASL, Irf3 and Irf4) in a cell or cells of the subject is regulated.

In a further aspect, the present invention relates to a method of regulating (e.g. downregulating) the expression of one or more pro-inflammatory genes (such as one or more genes selected from the group consisting of but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ, CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α in a cell or cells of a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), wherein the expression of one or more pro-inflammatory genes (such as one or more genes selected from the group consisting of but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α) in a cell or cells of the subject is regulated.

The present invention, in a further aspect, relates to a method of improving intestinal microbiota in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the intestinal microbiota in a subject is improved.

In another aspect, the present invention relates to a method of regulating appetite in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the appetite in the subject is regulated.

The present invention, in another aspect relates to a method of regulating (e.g. downregulating) the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of the subject is regulated.

In a further aspect, the present invention relates to a method of improving alimentary canal health in a subject, said method comprising administering a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein alimentary canal health in a subject is improved.

The present invention, in a further aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for modulating the inflammation of a tissue or an organ (such as the intestine) in a subject.

The present invention, in another aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for modulating the production of T cells (e.g. regulatory T cells such as regulatory T cells capable of expressing TLR5) in a subject.

In a further aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating the immune system of a subject.

The present invention, in a further aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for the treatment of a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder.

The present invention, in another aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for modulating dendritic cells (such as bone marrow dendritic cells) and/or epithelial cells in a tissue or an organ of a subject.

In another aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating the production of IL-10 and/or TGFβ in a cell or cells of a subject.

The present invention, in a further aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating the production of cell surface markers involved in immune responses and antigen recognition such as CD40, I-A/I-E, CD317/BST-2, CD103, CD80, CD86, CD83 and/or Siglec-H and/or the species equivalent in a cell or cells of a subject.

In a further aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating (e.g. downregulating) the expression of one of more Type I IFN genes (such as one or more genes selected from the group consisting of but not limited to IFN-β1, IFN-β3, Ifi202b, Ifi203, IFI44, IFTI, MXI, OASI, OAS2, OAS3, OASL, Irf3 and Irf4) in a cell or cells of a subject.

In another aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating (e.g. downregulating) the expression of one or more pro-inflammatory genes (such as one or more genes selected from the group consisting of but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α) in a cell or cells of a subject.

The present invention, in a further aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for improving intestinal microbiota in a subject.

The present invention, in another aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating appetite in a subject.

The present invention, in a further aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for regulating (e.g. downregulating) the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject.

The present invention, in another aspect, relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for improving alimentary canal health in a subject.

In another aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in medicine.

In a further aspect, the present invention relates to a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in restoring immunological tolerance.

In another aspect, the present invention relates to use of a Roseburia flagellin, and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for the manufacture of a medicament for restoring immunological tolerance in a subject.

The present invention relates to, in another aspect, a method of restoring immunological tolerance in a subject, said method comprising administering a Roseburia flagellin and/or a polynucleotide sequence encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and wherein the immunological tolerance in a subject is restored.

FIGURES

FIGS. 1A-1B. Sequence and annotation of R. hominis genome. The complete genome sequence of R. hominis A2-183 was produced. It is represented by a single 3,592,125-bp chromosome with four ribosomal operons, 66 RNAs and 3,273 predicted proteins. FIG. 1A R. hominis circular genome map with the location of the PCR experiments (Table S1) indicated in the regions targeted by the primers. The tracks on the genome map, starting at the outer track 0, are: track 0 (blue)—Real-time PCR experiments indicated by numbered tick marks; track 1 (pale blue)—Forward CDS; track 2 (pale blue)—Reverse CDS; track 3 (grey)—rRNA; track 4 (green)—tRNA; track 5 (red)—STS marking regions targeted by Real-time PCR; graph 1—GC content; graph 2—GC bias. (FIG. 1B) Functional annotation of the R. hominis genome shows that the largest number of genes belong to Carbohydrates, Protein Metabolism and Amino acids and Derivatives.

FIGS. 2A-2D. R. hominis responds to the gut environment by up-regulating motility, mobilization and chemotaxis genes. Germfree GF C3H/HeN male mice were given R. hominis culture by gavage for 28d, and compared to germfree control animals. At 14d and 28d, R. hominis-treated animals (N=5) and control animals (N=4) were sacrificed and ileum, colon and caecum were collected. FIG. 2A Real-time PCR validation of genes involved in conjugation/mobilization transfer. FIG. 2B Real-time PCR validation of genes involved in Motility and Chemotaxis. FIG. 2C Western blot of R. hominis grown in vitro in the presence of UV irradiated standard murine chow immuno-stained with affinity-purified Fla1 antibody, Fla2 specific antiserum and anti-DNA gyrase A antibody (lane 1: no diet, lane 2: 0.01 g diet/10 mL of R. hominis culture, lane 3: 0.02 g diet/10 mL, lane 4: 0.05 g diet/10 mL, lane 5: 0.1 g diet/10 mL, lane 6: 0.2 g diet/10 mL, lane 7: 0.5 g diet/10 mL, lane 8: 1 g diet/10 mL). Electron microscopy (EM) picture of R. hominis showing flagella (black arrows). Immunocytochemistry performed on bacteria from luminal contents of colonized mice and from R. hominis grown in vitro using FlaA1 and FlaA2 specific antiserum. Original magnification ×1000. FIG. 2D Real-time PCR validation of genes involved in butyrate metabolism. FIG. 2E Real-time PCR analysis of R. hominis transcripts during in vitro exposure to human intestinal epithelial cells. Real-time PCR results are presented as fold change, *P<0.05, **P<0.01, ***P<0.001.

FIGS. 3A-3C. Identification of transcripts differentially expressed in the murine gut after mono-association with R. hominis. FIG. 3A Affymetrix microarray analysis of differentially expressed genes in R. hominis-colonized mice (N=5) relative to GF (N=4). Bar graphs represent number of genes higher and lower expressed after 14 and 28 days. FIG. 3B Heatmap generated from differentially expressed genes with functional significance between GF and R. hominis-colonized mice at 14d and 28d. FIG. 3C Real-time PCR validation of genes shown to be significantly different between R. hominis-colonized and GF mice. Real-time PCR results are presented as fold change, *P<0.05, **P<0.01, ***P<0.001.

FIG. 4. Induction of FoxP3+ Treg cells by Roseburia hominis. Flow cytometry analysis of FoxP3+ Treg cells in lamina propria (P=0.0425 between control and R. hominis treatment) and mesenteric lymph nodes (P=0.0683) of conventional C3H/HeN treated for 14 days with R. hominis.

FIGS. 5A-5E. Colonic T cell markers are significantly induced by R. hominis mono-colonization. FIG. 5A is an Immunofluorescence analysis of ascending colon lamina propria cells with anti-CD3 and anti-FoxP3 in germfree and R. hominis mono-colonized C3H/HeN (N=8) and C57Bl/6 (N=3) mice. Immunofluorescence analysis of lamina propria cells labelled with FIG. 5B anti-Ly6G, FIG. 5C anti-CD11b, FIG. 5D anti-CD3, and FIG. 5E anti-CD3 and anti-FoxP3 in ascending colon of GF and R. hominis-treated C3H/HeN mice. Data expressed as number of positive cells per field of view in GF mice (N=7-8) and R. hominis-treated mice (N=8-10). *P<0.05. Original magnification ×630.

FIGS. 6A-6G. R. hominis flagellin RH1 has specific effects on intestinal epithelial cells and murine bone marrow-derived dendritic cells. FIG. 6A depicts a heatmap generated from differentially expressed genes in Caco-2 intestinal epithelial cells (N=1) treated with different bacterial flagellins Salmonella enteritidis (SE), E. coli K12 (EC), RH1 and RH2. FIGS. 6B-6D depict expression of (FIG. 6B) CD40; (FIG. 6C) I-A/I-E and (FIG. 6D) CD103 by CD11c+B220+CD317+ Flt3L− derived dendritic cells from conventional C3H/HeN, control (blue) and after 24 hrs incubation with recombinant flagellin (SE, K12, RH1, RH2, RI1, RI2, RI3, RI4, Er; green) determined by flow cytometry. Histogram represents data from three experiments. FIG. 6E depicts frequencies of recombinant flagellin (SE, K12, RH1, RH2) treated Flt3L- and GMCSF-derived dendritic cell populations from conventional C3H/HeN gated on CD11c+B220+CD317+ cells and CD11c+CD11b+B220− cells, respectively. Data presented as percentage of total, live and singlet cells, mean±SEM from three experiments. FIG. 6F depicts protein expression of cytokines IL-10 and IL-12 was measured by CBA in supernatants from control (unstimulated DCs; N=3) and RH1-treated DCs (N=3) derived from C3H/HeN and C57Bl/6. Data is presented as mean±SD. ***P<0.001. FIG. 6G depicts quantitative analysis of immunofluorescent labelling of ascending colon lamina propria cells with anti-CD3 and anti-FoxP3 in germfree and R. hominis mono-colonized TLRSKO mice (N=2) (SE): Salmonella enteritidis flagellin; (K12): Escherichia coli K12 flagellin; (Rh1): Roseburia hominis Fla1; (Rh2): Roseburia hominis Fla2; (Ri1): Roseburia intestinalis Fla1; (Ri2): Roseburia intestinalis Fla2; (Ri3): Roseburia intestinalis Fla3; (Ri4): Roseburia intestinalis Fla4; (Er) Eubacterium rectale flagellin.

FIGS. 7A-7C. R. hominis attenuates inflammation in an experimental model of colitis. Twenty-two female C57BL/6 mice were used to assess the therapeutic effect of R. hominis during DSS-induced colitis. Treated mice were dosed daily with 10⁹ CFU R. hominis for 14 days. From day 8, mice were given DSS in their drinking water for 6 days. The animals were euthanized on day 14 and intestinal tissue sampling was performed. FIG. 7A Untreated DSS mice (N=8) had strong elevation of all genes compared to control mice (N=4), while differential gene expression was lower in R. hominis-treated animals (N=10). Real-time PCR results are presented as fold change, ***P<0.001. FIG. 7B Histopathology tissue scoring presented as mean percentage of fields of view at a given grade. DSS treatment significantly altered all fields of view at grades 0, 2, 3, and 4. R. hominis significantly reduced the % fields of view for grade 4 pathology (p=0.02) and increased the % fields of view for grade 0. Data is presented as mean±SD. FIG. 7C Ascending colon (haematoxylin/eosin stained) of control, DSS-treated and DSS/R. hominis-treated IL-10KO animals. Images shown are representative fields of view from each treatment group. Original magnification ×100.

Supplementary Figures

FIGS. 8A-8C. R. hominis preferentially colonizes the ascending colon of mono-colonized mice. FIGS. 8A-8C R. hominis preferentially colonizes the ascending colon of mono-colonized mice. FIG. 8A R. hominis colonized the ascending colon of the mouse gut with close association of bacteria to the host epithelium, detected by FISH using A2-183 (R. hominis-specific probe; FITC), Eub338 (universal 16S probe; Cy3) and DAPI (nuclei; blue). Overlays of A2-183+Eub338 and Eub338+DAPI are also shown. The gamma for the red channel was increased in the Eub338+DAPI overlay to illustrate the labelled bacteria. Original magnification ×630. FIG. 8B PCR using R. hominis-specific primers showed a strong positive signal in faecal DNA post-colonization, while faeces of GF animals were negative for the presence of any bacteria. FIG. 8C Real-time PCR analysis showing colonization levels of R. hominis/g faeces. Bacterial DNA isolated from faeces was compared against known standard concentrations of R. hominis grown in culture. Similar bacterial levels were detected in all mono-colonized mice, approximating 1×10¹⁰ bacteria/g faeces. Faeces of GF animals tested negative for the presence of any bacteria.

FIGS. 9A-C. Gene Ontology analysis performed on genes up-regulated at 28 days in the ascending colon. Gene Ontology (GO) based functional interpretation of the data was performed using DAVID. Significantly different transcripts (P<0.05) were allocated into the GO category ‘Biological Process’ to find significantly enriched GO terms. The GO biological processes for ‘actin polymerization’ (GO:0030041) and ‘negative regulation of 1-kappaB kinase/NF-kappaB cascade’ (GO:0043124) were affected.

FIGS. 10A-10C. Identification of transcripts differentially expressed in the murine gut after mono-association with E. coli. FIG. 10A Affymetrix microarray analysis of differentially expressed genes in E. coli and R. hominis-colonized mice over time. Bar graphs represent number of genes higher and lower expressed after 22 and 28 day, respectively. FIG. 10B Heatmap generated from differentially expressed genes with functional significance in E. coli-colonized mice at 22 d vs. 10 d.

FIGS. 11A-11D. Identification of transcripts differentially expressed in TLRSKO mouse gut after mono-association with R. hominis. FIG. 11A Heatmap generated from differentially expressed genes in ascending colon of R. hominis-colonized TLRSKO (N=3) and wildtype mice (N=3) at 28 d. FIG. 11B Heatmap generated from differentially expressed immune-associated genes in ascending colon of R. hominis-colonized TLRSKO and wildtype mice at 28 d. FIG. 11C Heatmap generated from differentially expressed genes in ileum of R. hominis-colonized TLRSKO and wildtype mice at 28 d. FIG. 11D Heatmap generated from differentially expressed immune-associated genes in ileum of R. hominis-colonized TLRSKO and wildtype mice at 28 d.

FIGS. 12A-J. Gene Ontology analysis performed on genes down-regulated at 28 days in the ascending colon. GO biological processes involved in appetite regulation, such as ‘negative regulation of response to food’ (GO:0032096), ‘negative regulation of appetite’ (GO:0032099) and ‘regulation of catecholamine secretion’ (GO:0050433) were mostly affected. FIG. 12K depicts an overview of the arrangement of FIGS. 12A-J.

FIGS. 13A-13B. R. hominis colonization influences satiety genes and body weight. Dry body weight and lipid carcass analysis was performed. FIG. 13A Dry carcass weights of R. hominis-associated mice were significantly heavier compared to GF animals. FIG. 13B Carcass lipid analysis showed that total adiposity was also significantly higher in R. hominis-treated animals at 14d. Data is presented as mean±SD.

FIG. 14 Representation of the cloning vector pCR-Blunt II-TOPO used for cloning recombinant flagellins insoluble after cell lysis. It allows high-efficiency DNA cloning of blunt-end PCR products. It encodes Kanamycin and Zeocin resistance genes for selection in E. coli, and the insert is flanked by multiples restriction sites for excision.

FIG. 15 Representation of the expression vector T7-MAT-Tag-FLAG- used for cloning recombinant flagellins insoluble after cell lysis. The multi cloning site (MCS) is flanked by MAT (Metal Affinity Tag) sequence and FLAG peptide (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys; SEQ ID NO: 13) sequence, which results in the production of double-tagged flagellin, which can be further purified by affinity columns. This expression vector also encodes a pT7/lac (phage T7 lac operon) promoter for IPTG inducible, high-level expression of MAT-ORF-FLAG recombinant flagellins, an internal lad gene that represses transcription at basal state in any E. coli host, and an AmpR gene for ampicillin selection.

FIG. 16 Visualization on a SDS-PAGE of recombinant flagellin cloned with the pCR-Blunt II-TOPO cloning vector and expressed through the pT7-MAT-Tag-FLAG-2 expression vector. Description of lanes: 1, protein standard (kDa); 2, RH1.

FIG. 17 depicts a ribbon structure of R. hominis Fla1. The flagellin structure consists of four domains: DO, D1, D2 and D3.

FIGS. 18A and 18B show an SDS-Analysis of recombinant flagellins. FIG. 18(A) K12 (Escherichia coli K12); ER (Eubacterium rectale 33656); RI1 (Roseburia intestinalis Fla 1); RI2 (Roseburia intestinalis Fla 2); FIG. 18(B) RH1 (Roseburia hominis Fla 1); RH2 (Roseburia hominis Fla 2); RI3 (Roseburia intestinalis Fla 3); RI4 (Roseburia intestinalis Fla 4).

FIGS. 19-22. Multiple sequence alignment confirming flagellin nucleotide sequence and accession number.

FIG. 23 Comparative analysis of CCL20 gene induction by different flagellins. HT-29 and Caco-2 cells were stimulated for 2 hours with a single recombinant flagellin at a concentration of 100 ng/mL. Total RNA was extracted and subjected to real time quantitative PCR analysis for the genes CCL20 and β-actin. Experiments were done in triplicate on three separate occasions. Table D2 indicates significant differences between each treatment calculated with paired t test in HT-29.

FIG. 24 Flagellin-mediated chemokine secretion in HT-29 and Caco-2 cells. Tables D3a, D3b, D3c and D3d indicate significant differences between each treatment calculated with paired t test.

FIG. 25, neutralization of TLR5 with an anti-TLR5 specific antibody.

FIG. 26A: Frequencies of GM-CSF/IL-4 derived dendritic cells stimulated with recombinant flagellins, data shown as fold change compared to unstimulated GM-CSF/IL-4 derived dendritic cells. FIG. 26B: Frequencies of Flt3L derived dendritic cells stimulated with recombinant flagellins, data shown as fold change compared to unstimulated Flt3L derived dendritic cells.

FIGS. 27A and 27B Flow cytometry analysis of FoxP3+ Tregs in lamina propria of BOY/J WT and TLRSKO mice treated with R. hominis.

DETAILED DESCRIPTION Flagellin

Flagellin is the principal substituent of bacterial flagellum, and is present in large amounts on nearly all flagellated bacteria. Typically, flagellins are globular proteins which arrange into a hollow cylinder to form the filament in bacterial flagellum.

The diversity of flagellin structural proteins and gene sequences is well recognized and vary according to bacterial species, geographical and clinical and environmental origins. There are thousands of flagellins and related flagellin genes. Some of the important ones in gut bacteria include the flagellins FLA, FliC, FlgC, FLiE, FlaB, MoA and FliG.

There are several types of FLA (Fla) polypeptides. FlaA1, FlaA2, FlaA3, FlaA4 and FlaB are examples of FLA polypeptides.

Polypeptide FlaA1

The term “polypeptide FlaA1” as used herein refers to the flagellin protein FlaA1. Examples of such polypeptides include the FlaA1 polypeptide of Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, and Roseburia inuhnivorans; the polypeptide sequence shown as SEQ ID NO 2 or SEQ ID No 6; and polypeptides having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO 2 or SEQ ID No 6 or variants, homologues, fragments or derivatives thereof.

SEQ ID NO 2 has the following sequence:

TABLE-US-00001 MVVQHNLTAMNANRQLGITTGAQAKSSEKLSSGYKINRAADDAAGLTISE KMRSQVRGLNKASDNAQDGVSLIQVAEGALSETHSILQRMNELATQAAND TNTTSDRTAVQQEINQLASEITRIASTTQFNTMNLIDGNFTSKKLQVGSL CGQAITIDISDMSATGLGVSGLVVSSFSAAGKAMSAAQDAISYVSSMRSK LGALQNRLEHTISHLDNISEHTSSAESRIRDTDMAEEMVEYSKNNILAQA GQSMLAQANQSTQGVLSLLQ SEQ ID NO 2 is deposited with NCBI under accession number ABI48297.1.

The terms “polypeptide FlaA1” and “FlaA1 polypeptide” are used interchangeably herein.

The terms “FlaA1”, “Fla1” and “RH1” may be used interchangeably herein.

In one embodiment, the polypeptide FlaA1 has at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO 2 or to variants, homologues, fragments or derivatives thereof. In one aspect, the amino acids at positions 79 to 117 and positions 408 to 439 as well as 411, 412, 420 of SEQ ID NO 2 (or equivalent thereof) are considered important. In one aspect, the amino acids at positions 411, 412, 420 of SEQ ID NO 2 (or equivalent thereof) are alanine (A), glutamine (Q) and serine (S) respectively.

In one embodiment, the polypeptide FlaA1 is the polypeptide shown as SEQ ID NO 2 or SEQ ID No 6.

FlaA1 polypeptides can be derived from certain microorganisms. In one aspect, the FlaA1 polypeptide is derived from a bacterium such as a Firmicute. In a further aspect, the FlaA1 polypeptide is derived from a Roseburia spp such as a Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, or Roseburia inulinivorans.

Roseburia hominis and Roseburia intestinalis are recently described commensal gut anaerobes of the phylogenetic cluster XIVa within the Firmicutes phylum, belonging to a dominant group of bacteria in the human gut and are also major butyrate producers. An example of Roseburia hominis is the strain deposited at National Collections of Industrial, Food and Marine Bacteria (NCIMB) at NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen, UK, AB21 9YA, on 21 Oct. 2004 by the Rowett Research Institute under the accession number NCIMB 14029.sup.T Roseburia hominis A2-183.sup.T (DSM=16839.sup.T). Another example is the bacterial species is Roseburia hominis as described in Duncan, S. H., Aminov, R. I., Scott, K. P., Louis, P., Stanton, T. B., & Flint, H. J. (2006) Int. J. Syst. Evol. Microbiol. 56: 2437-2441. An example of Roseburia intestinalis is the strain deposited under the accession number NCIMB 13810 Roseburia intestinalis L1-82.sup.T (DSM=14610.sup.T) Another example is the bacterial species is Roseburia hominis as described in Duncan, S. H., Aminov, R. I., Scott, K. P., Louis, P., Stanton, T. B., & Flint, H. J. (2006) Int. J. Syst. Evol. Microbiol. 56: 2437-2441. Deposited strains NCIMB 14029 and NCIMB 13810 were deposited under the terms of the Budapest Treaty. Viability for each Roseburia hominis strain deposited under the terms of the Budapest Treaty is assured. Maintenance of a viable culture is assured for 30 years from the date of deposit. During the pendency of the application, access to the deposit will be afforded to one determined by the Commissioner of the United States Patent and Trademark Office to be entitled thereto. All restrictions on the availability to the public of the deposited microorganisms will be irrevocably removed upon the granting of a patent for this application. The deposit will be maintained for a term of at least thirty (30) years from the date of the deposit or for the enforceable life of the patent or for a period of at least five (5) years after the most recent request for the furnishing of a sample of the deposited material, whichever is longest. The deposit will be replaced should it become necessary due to inviability, contamination or loss of capability to function in the manner described in the specification.

The term “polynucleotide sequence encoding the polypeptide FlaA1” as used herein refers a polynucleotide sequence encoding the flagellin protein FlaA1. Examples of such polynucleotide sequences include the gene FlaA1 of R. hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, or Roseburia inulinivorans; the polynucleotide sequence shown as SEQ ID NO 1 or SEQ ID No 5; polynucleotide sequences encoding the polypeptide shown as SEQ ID NO 2 or SEQ ID No 6; polynucleotides sequences having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO 1 or SEQ ID No 5 or variants, homologues, fragments or derivatives thereof; and polynucleotides sequences encoding the polypeptide shown as SEQ ID NO 2 or SEQ ID No 6 or encoding a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polypeptide shown as SEQ ID NO 2 or SEQ ID No 6 or variants, homologues, fragments or derivatives thereof.

SEQ ID NO 1 has the following sequence:

TABLE-US-00002 ATGGTAGTACAGCACAATCTTACAGCAATGAACGCTAACAGACAGTTAGG TATCACAACAGGCGCACAGGCTAAGTCTTCTGAGAAGTTATCTTCTGGTT ACAAGATCAACCGCGCAGCAGATGACGCAGCAGGTCTTACGATTTCCGAG AAGATGAGAAGCCAGGTTAGAGGCTTAAATAAAGCTTCTGACAACGCACA GGATGGTGTATCCCTTATTCAGGTAGCTGAGGGTGCATTAAGTGAGACAC ACTCCATCTTACAGCGTATGAATGAGTTAGCAACTCAGGCAGCAAACGAT ACCAATACAACCTCAGACAGAACTGCAGTTCAGCAGGAGATCAACCAGTT AGCATCTGAGATCACCAGAATCGCTTCTACAACTCAGTTCAACACAATGA ACCTGATCGATGGTAACTTCACAAGTAAGAAGCTTCAGGTAGGTTCCCTT TGCGGACAGGCTATCACAATCGATATCTCTGATATGTCTGCTACAGGTCT TGGCGTTAGCGGATTAGTAGTATCTTCCTTCTCTGCAGCTGGTAAGGCAA TGTCTGCAGCTCAGGATGCTATCAGCTACGTATCTTCTATGCGTTCTAAG CTGGGTGCATTACAGAACAGACTTGAGCACACAATCTCCCACCTGGACAA CATTTCTGAGCACACATCTTCTGCAGAGTCTCGTATCCGTGATACAGATA TGGCTGAAGAGATGGTTGAGTACAGCAAGAACAACATCCTTGCTCAGGCA GGACAGTCTATGCTTGCTCAGGCTAACCAGTCTACTCAGGGTGTATTATC CTTATTACAGTAA SEQ ID NO 1 is deposited with NCBI under accession number DQ789140.1.

In one embodiment, the polynucleotide sequence encoding the polypeptide FlaA1 has at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polynucleotide sequence shown as SEQ ID NO 1 or SEQ ID No 5 or to variants, homologues, fragments or derivatives thereof.

In one embodiment, the polynucleotide sequence encoding the polypeptide FlaA1 encodes a polypeptide shown as SEQ ID NO 2 or SEQ ID No 6 or a polypeptide having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to the polypeptide shown as SEQ ID NO 2 or SEQ ID No 6 or to variants, homologues, fragments or derivatives thereof.

In one embodiment, the polypeptide FlaA1 is a truncated FlaA1 polypeptide. For example, the truncated polypeptide comprises at least 20, 30, 40, 50, 75, 100, 125, 150, 175 or 200 amino acids of polypeptide shown as SEQ ID NO 2 or SEQ ID No 6.

Without wishing to be bound by theory, two essential regions of flagellin protein involved in the recognition and activation of TLR5 are amino acids 79-117 of SEQ ID NO 2 (N-D1 domain) and amino acids 408-439 of SEQ ID NO 2 (C-D1 domain). Without wishing to be bound by theory, amino acid: A411, Q412, 5420 are important amino acids.

Examples of truncated FlaA1 polypeptides include: polypeptides which comprise amino acids 79-117 and amino acids 408-439 of SEQ ID NO 2; polypeptides having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to amino acids 79-117 and amino acids 408-439 of SEQ ID NO 2; polypeptides having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to amino acids 79-117 and amino acids 408-439 of SEQ ID NO 2 wherein the amino acid at position 411 (or equivalent thereto) is alanine (A) and/or the amino acid at position 214 is glutamine (Q) and/or the amino acid at position 420 is serine (S); polypeptides comprising amino acids 79-439 of SEQ ID NO 2; polypeptides comprising amino acids 79-439 of SEQ ID NO 2 wherein the amino acid at position 411 (or equivalent thereto) is alanine (A); polypeptides having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to amino acids 79-439 of SEQ ID NO 2; and polypeptides having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to amino acids 79-439 of SEQ ID NO 2 wherein the amino acid at position 411 (or equivalent thereto) is alanine (A) and/or the amino acid at position 214 is glutamine (Q) and/or the amino acid at position 420 is serine (S).

In one aspect, the amino acids at positions 411, 412, 420 of SEQ ID NO 2 (or equivalent thereof) in a truncated FlaA1 polypeptide are alanine (A), glutamine (Q) and serine (S) respectively.

In one embodiment, the polynucleotide sequence encoding the polypeptide FlaA1 encodes a truncated FlaA1 polypeptide.

In one embodiment, the polypeptide FlaA1 is a fusion polypeptide. For example, the polypeptide is fused to glutathione S-transferase (GST).

Roseburia Genus

Roseburia bacteria are slightly curved rod-shaped cells that are strictly anaerobic and indigenous to the mammalian intestine. The bacteria are butyrate-producing and are actively motile through multiple flagella present along the concave side and in a cluster at one end (Stanton and Savage 1983). Currently, within the Roseburia genus, five species have been identified and characterised: Roseburia cecicola, Roseburia faecis, Roseburia hominis, Roseburia intestinalis, and Roseburia inuhnivorans (Stanton and Savage 1983, Duncan et al 2006).

-   Stanton and Savage (1983—Roseburia cecicola gen. nov., sp. nov., a     motile, obligately anaerobic bacterium from a mouse cecum. Int. J.     Syst. Bacteriol., 1983, 33, 618-627.) describe Roseburia cecicola. -   Duncan et al. (2006—Proposal of Roseburia faecis sp. nov., Roseburia     hominis sp. nov. and Roseburia inuhnivorans sp. nov., based on     isolates from human faeces. Int. J. Syst. Evol. Microbiol., 2006,     56, 2437-2441) describe Roseburia faecis. -   Duncan et al. (2006—Proposal of Roseburia faecis sp. nov., Roseburia     hominis sp. nov. and Roseburia inuhnivorans sp. nov., based on     isolates from human faeces. Int. J. Syst. Evol. Microbiol., 2006,     56, 2437-2441) describe Roseburia hominis. -   Duncan et al. (2002 —Roseburia intestinalis sp. nov., a novel     saccharolytic, butyrate-producing bacterium from human faeces.     Int. J. Syst. Evol. Microbiol., 2002, 52, 1615-1620) describe     Roseburia intestinalis. -   Duncan et al. (2006—Proposal of Roseburia faecis sp. nov., Roseburia     hominis sp. nov. and Roseburia inulinivorans sp. nov., based on     isolates from human faeces. Int. J. Syst. Evol. Microbiol., 2006,     56, 2437-2441) describe Roseburia inulinivorans.

Roseburia Flagellin

The term “Roseburia flagellin” as used herein refers to a flagellin protein derived or derivable from a Roseburia bacterium such as Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, and Roseburia inulinivorans.

The Roseburia flagellin may be flaA1, flaA2, flaA3, flaA4 or combinations thereof.

The terms “FlaA1”, “Fla1”, “flaA1” and “fla1” are used interchangeably herein.

The terms “FlaA2”, “Fla2”, “flaA2” and “fla2” are used interchangeably herein.

The term Fla is used herein to encompass the polypeptides that may be flaA1, flaA2, flaA3 flaA4 or fliC.

In one embodiment, the present invention encompasses the use of at least one Roseburia flagellin. For example, the present invention encompasses the use of a combination of at least two, at least three, at least four, or at least five Roseburia flagellins.

In some embodiments, the combination of Roseburia flagellins comprises flagellins which are derived or derivable from at least two, three, four or five different Roseburia species.

Examples of Roseburia flagellins include flagellins derived or derivable from Roseburia bacterium such as Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, and Roseburia inulinivorans. In one embodiment, the flagellin is derived or derivable from Roseburia hominis. In another embodiment, the flagellin is derived or derivable from Roseburia intestinalis.

Examples of Roseburia flagellins include polypeptide sequences having at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identity to SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12 or variants, homologues, fragments or derivatives thereof.

In one embodiment, the Roseburia flagellin has the polypeptide sequence shown as SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12.

Examples of Roseburia hominis flagellins are Roseburia hominis Fla1 and Fla2.

An example of Roseburia hominis Fla1 is shown as SEQ ID NO 2. Roseburia hominis Fla1 is also referred herein as RhFlaA1, RHFlaA1, RhFla1, RHFla1, RH1 or Rh1.

SEQ ID NO 2 has the following sequence:

TABLE-US-00003 MVVQHNLTAMNANRQLGITTGAQAKSSEKLSSGYKINRAADDAAGLTISE KMRSQVRGLNKASDNAQDGVSLIQVAEGALSETHSILQRMNELATQAAND TNTTSDRTAVQQEINQLASEITRIASTTQFNTMNLIDGNFTSKKLQVGSL CGQAITIDISDMSATGLGVSGLVVSSFSAAGKAMSAAQDAISYVSSMRSK LGALQNRLEHTISHLDNISEHTSSAESRIRDTDMAEEMVEYSKNNILAQA  GQSMLAQANQSTQGVLSLLQ SEQ ID NO 2 is deposited with NCBI under accession number ABI48297.1.

An example of Roseburia hominis Fla2 is shown as SEQ ID NO 4. Roseburia hominis Fla2 is also referred herein as RhFlaA2, RHFlaA2, RhFla2, RHFla2, Rh2 or RH2.

SEQ ID NO 4 has the following sequence:

TABLE-US-00004 MVVNHNMAAICESRQLRYNVKKMEKSSKKLATGYKLNTANDDAAGLQISE TMRHHVKGLNKASRNSQDGISMLQTADAALQETQDVLDRMVELTTQAAND INTDSDRRAIQDELDQLNKEVDRIAYTTHFNQQYMLAEGTPQAAPGYYRI QSGALNGQAIDIHFVNASKESLGTDKVNVSSHAKASESITMVQDAIEQAA LWRDEFGSQQERLEHAVRNTDNTSQNTQSAESGIRDTNMNMEMVLYSTNR ILVHASQSILAQYNDDAKSVLEILK

Examples of Roseburia intestinalis flagellins include Roseburia intestinalis Fla1, Fla2, Fla3 and Fla4.

An example of Roseburia intestinalis Fla1 is shown as SEQ ID No 6. Roseburia intestinalis is also referred herein as RiFlaA1, RIFlaA1, RiFla1, RIFla1, Ri1 or RI1.

SEQ ID NO 6 has the following sequence:

TABLE-US-00005 MRINYNVSAAIANKHLLGIEDNLSASMERLSSGLKINHSKDNPAGMAISN KMKAQIDGLNRASQNASDGISVIQIADGALSETTSILQRMRELSVQAASD ATMTPADKEAIQKEITSLKDEVDRISTDTEYNSKTLLDGSLDTRVYTKNA TRVDISDHVKAGQYQLSIDTAATQAGPVTANQNYNSTAPVGASGTMSING SKVEIEAADTYAEAFEKIRNAAETGETTVKIEKNGALSETAEQYGMSSIL EIAFDDKQLANALGETADGGNSVVEDPENKGSYVYGQIQNGKVIVPSGTD AEVTLTKPSDGTGEGDTATVKTDGNKITVTDRAGFEMSFLADAGYTGKLD FDVTDIGTMALHIGANEDQETRVRIPEVSCKSLYIDDADVTTVNGAGRGI TQFDDAISKVSEVRSRLGAYQNRLESTVSSLDTFEENMTGAQSRLTDADM ASEMTDYTHQNVLNQAAISVLTQANDLPQ

An example of Roseburia intestinalis Fla2 is shown as SEQ ID No 8. Roseburia intestinalis Fla2 is also referred herein as RiFlaA2 or RIFlaA2 or Ri2 or RI2.

SEQ ID NO 8 has the following sequence:

TABLE-US-00006 MVVNIHNMALICESRQLRCNVKNMEKSSKKLATGYKLLGANDDAAGLQISE TMRHQTRGLNKASRNSQDGISMLQTADAALQETQEVLDRMTDLTTQAAND INTDADRRAIQDEIDQLNQEVDRIAYTTNFNQQYILADGTPQARPGYYMI QTGSLAGQGIEIKFVNASKESLGVDKVDVSSHAKATESIAVVQNAIEKAA SFRDTFGAQQERLEHALRGTDNTSESTQRAESSRRDTNMNMEMVQYSTNR ILVQASQSILAQYNDDAKYVLEMLKQVLQILQ

An example of Roseburia intestinalis Fla3 is shown as SEQ ID No 10. Roseburia intestinalis Fla3 is also referred herein as RiFla3 or RIFla3 or Ri3 or RI3.

SEQ ID NO 10 has the following sequence:

TABLE-US-00007 MVVQHNMTAMNANRMLGVTTSAQAKSSEKLSSGYRINRAGDDAAGLTISE KMRSQIRGLNKASDNAQDGISLIQVAEGALSETHSILQRMNELATQAAND TNTTADRGAIQDEINQLTSEINRISSTTQFNTQNLIDGTFANKNLQVGSI CGQRITVSIDSMSAGSLNVSANLVKVNTFSAAGEAMSNIQGAISAISTQR SYLGALQNRLEHTISNLDNISENTQSAESRIRDTDMAEEMVTYSKNNILA QAGQSMLAQANQSTQGVLSLLQ

An example of Roseburia intestinalis Fla4 is shown as SEQ ID No 12. Roseburia intestinalis Fla4 is also referred herein as RiFla4 or RIFla4 or Ri4 or RI4.

SEQ ID NO 12 has the following sequence:

TABLE-US-00008 MAMVVQHNMSAMNANRNLGVTTGMQAKSSEKLSSGYKINRAADDAAGLSI SEKMRSQIRGLNKASDNAQDGISLIQTAEGALNESHSILQRMRELSVQAA NGTETDDDREAVQNEVSQLQEELTRISETTEFNTMKLLDGSQSGSTSSTG SGPKFGVVDATLDGALVTSNVKGIKVATAAATTTKAGQETAIWAADGKTL TLNLSKNKVYTQDEIDDLIANAKQEDSSATGAPAEVKVSLKNGIFNADAD TTAGTVTAGGVKAVSDEGTVTGFVGADTISETANKYGAEFNDTVEKEKED KAAGKEEVETNTAIEIDGANAVTAGEYTIHLAAGKEYTAEDLEDVLKTAG FDFDVKLSGNTPDEPNTLFATSGASTVTDITMGAGTAGAGLGSTDAMWGQ AGYDSVSSGAGITLQIGANEGQTMSFSIDDMSARALGVDGNKVDLSTQAG NAQKATDTIDAAIKKVSAQRGRMGAIQNRLEHTISLDTAAENTQTAESRI RDTDMAEEMVEYSKNNILAQAGQSMLAQANQSTQGVLSLLQ

The terms “polypeptide FlaA1”, “FlaA1 polypeptide”, “polypeptide Fla1” and “Fla1 polypeptide” are used interchangeably herein. The terms “polypeptide Fla2” and “Fla2 polypeptide” are used interchangeably herein. The terms “polypeptide Fla3” and “Fla3 polypeptide” are used interchangeably herein. The terms “polypeptide Fla4” and “Fla4 polypeptide” are used interchangeably herein.

In one aspect, the Roseburia flagellin is selected from the group consisting of Fla1, Fla2, Fla3 and Fla4. In one embodiment, the Roseburia flagellin is selected from the group consisting of Fla2, Fla1, Fla4 and combinations thereof. In a further embodiment, the Roseburia flagellin is Fla2.

In one aspect, the Roseburia flagellin is selected from the group consisting of Roseburia hominis Fla1, Roseburia hominis Fla2, Roseburia intestinalis Fla1, Roseburia intestinalis Fla2, Roseburia intestinalis Fla3 and Roseburia intestinalis Fla4. In one embodiment, the Roseburia flagellin is selected from the group consisting of Roseburia hominis Fla2, Roseburia intestinalis Fla2, Roseburia intestinalis Fla1, Roseburia intestinalis Fla4 and combinations thereof. In a further embodiment, the Roseburia flagellin is selected from the group consisting of Roseburia hominis Fla2, Roseburia intestinalis Fla2 and combinations thereof. In another embodiment, the Roseburia flagellin is Roseburia intestinalis Fla2.

In one embodiment, the present invention encompasses the use of at least one polynucleotide sequence encoding a Roseburia flagellin. For example, the present invention encompasses the use of a combination of at least two, at least three, at least four, or at least five polynucleotide sequences encoding Roseburia flagellins.

In one embodiment, the present invention encompasses the use of a polynucleotide sequence encoding at least one Roseburia flagellin. For example, the present invention encompasses the use of a polynucleotide sequence encoding a combination of at least two, at least three, at least four, or at least five polypeptide sequences encoding Roseburia flagellins.

The polynucleotide sequence encoding a Roseburia flagellin may encode flaA1, flaA2, fla3, fla4 or combinations thereof.

In some embodiments, the combination of polynucleotide sequences encoding Roseburia flagellins comprises polynucleotide sequences encoding flagellins which are derived or derivable from at least two, three, four or five different Roseburia species.

In some embodiments, the polynucleotide sequence encodes a combination of Roseburia flagellins which are derived or derivable from at least two, three, four or five different Roseburia species.

In another embodiment, the present invention encompasses the use of a combination of at least one Roseburia flagellin and at least one polynucleotide sequence encoding a Roseburia flagellin.

Examples of polynucleotide sequence encoding Roseburia flagellins include flagellins derived or derivable from Roseburia bacterium such as Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, and Roseburia inulinivorans. In one embodiment, the polynucleotide sequence encodes a Roseburia flagellin derived or derivable from Roseburia hominis. In another embodiment, the polynucleotide sequence encodes a Roseburia flagellin derived or derivable from Roseburia intestinalis.

Examples of polynucleotide sequences encoding Roseburia flagellin include the polynucleotide sequences encoding a polypeptide which has at least 75% identity to SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12 or variants, homologues, fragments or derivatives thereof and polynucleotide sequences having at least 75% identity to SEQ ID NO 1, SEQ ID NO 3, SEQ ID NO 5, SEQ ID NO 7, SEQ ID NO 9 or SEQ ID NO 11 or variants, homologues, fragments or derivatives thereof.

In one embodiment, the polynucleotide sequence encoding Roseburia flagellin has the polynucleotide sequence encoding a polypeptide which has the sequence shown as SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12.

In one embodiment, the polynucleotide sequence encoding the Roseburia flagellin has the polynucleotide sequence shown as SEQ ID NO 1, SEQ ID NO 3, SEQ ID NO 5, SEQ ID NO 7, SEQ ID NO 9 or SEQ ID NO 11.

Examples of polynucleotide sequences encoding Roseburia hominis flagellins are polynucleotide sequences encoding Roseburia hominis Fla1 and Fla2.

An example of a polynucleotide sequence encoding Roseburia hominis Fla1 is shown as SEQ ID NO 1.

SEQ ID No 1 has the following sequence:

TABLE-US-00009 ATGGTAGTACAGCACAATCTTACAGCAATGAACGCTAACAGACAGTTAGG TATCACAACAGGCGCACAGGCTAAGTCTTCTGAGAAGTTATCTTCTGGTT ACAAGATCAACCGCGCAGCAGATGACGCAGCAGGTCTTACGATTTCCGAG AAGATGAGAAGCCAGGTTAGAGGCTTAAATAAAGCTTCTGACAACGCACA GGATGGTGTATCCCTTATTCAGGTAGCTGAGGGTGCATTAAGTGAGACAC ACTCCATCTTACAGCGTATGAATGAGTTAGCAACTCAGGCAGCAAACGAT ACCAATACAACCTCAGACAGAACTGCAGTTCAGCAGGAGATCAACCAGTT AGCATCTGAGATCACCAGAATCGCTTCTACAACTCAGTTCAACACAATGA TACCTGATCGATGGAACTTCACAAGTAAGAAGCTTCAGGTAGGTTCCCTT TGCGGACAGGCTATCACAATCGATATCTCTGATATGTCTGCTACAGGTCT TGGCGTTAGCGGATTAGTAGTATCTTCCTTCTCTGCAGCTGGTAAGGCAA TGTCTGCAGCTCAGGATGCTATCAGCTACGTATCTTCTATGCGTTCTAAG CTGGGTGCATTACAGAACAGACTTGAGCACACAATCTCCCACCTGGACAA CATTTCTGAGCACACATCTTCTGCAGAGTCTCGTATCCGTGATACAGATA TGGCTGAAGAGATGGTTGAGTACAGCAAGAACAACATCCTTGCTCAGGCA GGACAGTCTATGCTTGCTCAGGCTAACCAGTCTACTCAGGGTGTATTATC CTTATTACAGTAA

An example of a polynucleotide sequence encoding Roseburia hominis Fla2 is shown as SEQ ID NO 3.

SEQ ID No 3 has the following sequence:

TABLE-US-00010 ATGGTGGTTAATCATAATATGGCGGCAATCTGTGAGAGCAGGCAGCTGCG CTATAACGTGAAGAAGATGGAAAAATCTTCCAAAAAGCTTGCGACAGGGT ACAAGCTGAACACAGCAAATGATGATGCGGCAGGCTTGCAGATATCAGAG ACGATGCGGCATCATGTGAAAGGGCTGAACAAAGCCTCCCGGAATTCACA GGACGGCATCAGTATGCTGCAGACGGCGGATGCAGCGCTCCAAGAGACGC AGGATGTTCTCGATCGTATGGTGGAGCTGACGACGCAGGCAGCCAATGAC ATCAACACAGACTCGGATCGCAGGGCTATTCAGGATGAGTTGGATCAGCT GAACAAGGAAGTGGACCGCATCGCCTATACGACGCACTTCAATCAGCAGT ATATGTTGGCGGAGGGAACGCCGCAGGCGGCACCGGGATATTACCGCATA CCAGTCCGGGGCACTGAAGGACAGGCGATAGATATCCATTTTGTAAATGC GAGCAAGGAGAGCCTTGGCACAGACAAAGTGAATGTATCTTCGCATGCGA AGGCGTCGGAATCCATCACGATGGTTCAGGACGCGATTGAACAGGCGGCG CTCTGGAGAGACGAGTTCGGCAGCCAGCAGGAGCGTCTGGAACATGCCGT GCGCAATACGGACAACACATCACAAAATACGCAGAGTGCGGAGTCAGGGA TCAGAGACACCAACATGAATATGGAGATGGTATTATATTCGACCAACCGG ATTCTGGTGCATGCATCCCAGAGTATTCTGGCACAGTATAATGATGATGC AAAATCAGTGCTTGAGATTTTGAAATAG

Examples of polynucleotide sequences encoding Roseburia intestinalis flagellins are polynucleotide sequences encoding Roseburia intestinalis Fla1, Fla2, Fla3 and Fla4.

An example of a polynucleotide sequence encoding Roseburia intestinalis Fla1 is shown as SEQ ID NO 5.

SEQ ID No 5 has the following sequence:

TABLE-US-00011 ATGCGTGGCGGAGACAATAGAAGGAGAAACAGAATGAGAATTAATTACAA TGTGTCAGCAGCGATTGCGAATAAACATTTACTTGGAATTGAGGATAATT TAAGTGCATCGATGGAACGGCTTTCATCGGGACTTAAGATCAACCATTCC AAGGACAATCCGGCAGGAATGGCTATTTCCAACAAGATGAAAGCACAGAT GTGATGGTTTAAACCGGGCTTCCCAGAATGCATCGGATGTATTTCTGTTA TTCAGATCGCAGATGGTGCGCTGAGTGAAACGACCAGTATTTTACAGCGT ATGAGAGAACTTTCCGTGCAGGCAGCGAGTGATGCAACAATGACACCGGC AGGATAAGAAGCAATCCAGAAAGAAATCACTTCATTAAAAGATGAAGTTG ACCGTATTTCTACAGATACAGAGTATAACAGCAAAACACTTTTAGATGGT TCATTAGATACCAGGGTTTACACCAAAAATGCAACAAGAGTGGACATTTC TGATCATGTGAAAGCAGGACAGTATCAGCTTTCCATTGATACTGCAGCTA CACAGGCCGGACCGGTAACAGCAAATCAGAATTATAATTCCACAGCACCG GTCGGTGCGTCCGGAACAATGAGTATTAATGGTTCTAAAGTAGAGATAGA GGCAGCCGACACCTATGCGGAGGCTTTTGAGAAGATCAGAAATGCAGCAG AGACTGGTGAAACAACCGTTAAGATTGAAAAGAATGGAGCACTTTCATTT ACCGCAGAACAGTACGGAATGTCAAGCATCTTAGAGATCGCATTNNTGAT GATAAGCAGCTTGCTAATGCACTTGGATTTACAGCAGACGGAGGAAACAG TGTTGTAGAAGATCCAGAGAATAAAGGCAGCTATGTATACGGACAGATTC AGAATGGCAAAGTGATCGTACCTTCCGGTACAGATGCCGAAGTAACGCTC ACAAAACCGAGTGATGGAACCGGATTTGGTGATACAGCTACGGTAAAAAC AGATGGAAATAAGATTACGGTTACAGACAGAGCCGGATTTGAGATGTCAT TTCTTGCTGATGCAGGTTATACGGGTAAGCTGGATTTTGATGTCACGGAT ATCGGAACGATGGCACTTCATATTGGAGCAAATGAGGATCAGGAAACAAG AGTGCGTATTCCGGAGGTTTCCTGCAAGAGCCTTTACATTGATGATGCAG ACGTGACGACTGTAAATGGAGCAGGCAGAGGTATCACACAGTTTGACGAT GCCATTTCAAAGGTCAGTGAAGTGCGTTCAAGACTTGGTGCATACCAGAA TCGTCTTGAGAGTACGGTATCAAGCCTGGATACGTTTGAAGAAAATATGA CAGGAGCCCAGTCACGACTGACAGATGCGGATATGGCATCGGAAATGACA GATTATACACATCAGAATGTATTAAATCAGGCAGCAATCTCTGTTTTGAC ACAGGCAAACGATCTGCCACAGCAGGTATTGCAGATTCTGCAGTAA

An example of a polynucleotide sequence encoding Roseburia intestinalis Fla2 is shown as SEQ ID NO 7.

SEQ ID No 7 has the following sequence:

TABLE-US-00012 ATGGTAGTTAATCATAATATGGCATTGATCTGTGAGAGTAGACAGTTACG ATGTAATGTGAAGAACATGGAGAAGTCTTCAAAAAAGCTGGCAACAGGTT ATAAATTGCTTGGAGCAAATGATGATGCAGCAGGATTACAGATATCAGAA ACCATGCGTCATCAGACCAGAGGTCTTAACAAAGCATCCAGAAATTCGCA AGATGGAATTAGTATGCTGCAGACAGCAGATGCAGCATTACAGGAGACAC AGGAAGTGTTGGATCGAATGACGGATCTGACAACACAGGCAGCTAATGAT ATCAATACGGATGCGGATCGTCGTGCAATTCAGGATGAAATCGATCAGTT AAATCAGGAAGTGGATCGTATTGCATATACGACGAATTTTAATCAGCAGT ATATATTAGCGGATGGAACTCCGCAGGCAAGACCAGGATACTATATGATA CAGACAGGAAGTCTTGCGGGACAGGGAATAGAGATTAAGTTTGTTAATGC GAGCAAAGAGAGCTTGGGTGTGGACAAGGTTGATGTATCATCGCATGCAA AAGCGACAGAATCTATAGCAGTGGTACAGAATGCAATTGAAAAGGCAGCT TCGTTTAGAGATACATTTGGGGCACAACAGGAGCGGTTAGAACACGCATT GCGTGGAACGGATAATACATCAGAAAGTACACAGAGGGCAGAATCAAGTA GACGCGATACCAACATGAATATGGAGATGGTACAATATTCTACAAACCGT ATTTTAGTACAGGCATCTCAGAGTATTTTAGCACAGTACAATGATGATGC AAAATATGTGTTGGAAATGTTAAAATAG

An example of a polynucleotide sequence encoding Roseburia intestinalis Fla3 is shown as SEQ ID NO 9.

SEQ ID No 9 has the following sequence:

TABLE-US-00013 ATGGTAGTACAGCACAATATGACCGCAATGAATGCGAACAGAATGTTAGG CGTTACAACAAGCGCACAGGCAAAATCTTCAGAGAAATTATCTTCTGGTT ACAGAATCAACCGTGCAGGTGATGACGCTGCTGGTTTAACAATTTCTGAG AAGATGAGAAGCCAGATCCGTGGATTAAACAAAGCTTCTGACAACGCACA GGATGGTATTTCCTTAATCCAGGTTGCTGAGGGTGCATTATCTGAGACAC ATTCTATCTTACAGCGTATGAATGAGTTAGCTACTCAGGCTGCTAACGAT ACCAATACAACTGCTGATAGAGGAGCTATTCAGGATGAGATCAACCAGTT AACATCTGAGATTAACAGAATCTCTTCTACAACTCAGTTCAATACTCAGA ACCTCATCGATGGTACATTCGCAAATAAAAACCTTCAGGTTGGTTCTATC TGTGGACAGAGAATTACTGTTTCTATCGACAGTATGTCTGCTGGTAGCTT AAATGTATCTGCTAACTTAGTAAAGGTTAACACTTTCAGTGCAGCAGGTG AAGCAATGTCCAATATTCAGGGTGCTATTTCTGCAATTTCTACACAGCGT TCTTACTTAGGAGCTCTTCAGAATCGTCTGGAGCATACAATCTCCAACTT GGACAACATTTCTGAGAATACTCAGTCTGCTGAATCTCGTATCCGTGATA CAGATATGGCTGAAGAGATGGTTACTTACAGCAAGAACAATATTCTTGCT CAGGCAGGACAGTCTATGCTTGCTCAGGCTAACCAGTCTACTCAGGGTGT ACTTTCTCTGTTACAGTAA

An example of a polynucleotide sequence encoding Roseburia intestinalis Fla4 is shown as SEQ ID NO 11.

SEQ ID No 11 has the following sequence:

TABLE-US-00014 ATGGCAATGGTAGTACAGCACAACATGTCCGCAATGAATGCGAACAGAAA TTTAGGTGTTACAACAGGAATGCAGGCAAAATCATCAGAGAAGTTATCTT CCGGTTACAAGATCAACCGTGCAGCAGATGATGCAGCAGGACTTTCTATT TCTGAGAAGATGAGAAGCCAGATCCGCGGTTTAAATAAAGCATCTGACAA TGCACAGGATGGTATCTCTTTAATCCAGACCGCTGAGGGAGCATTAAATG AGTCCCACTCTATTTTACAGAGAATGAGAGAGTTATCCGTACAGGCAGCC AACGGTACAGAGACAGATGACGACCGCGAGGCAGTACAGAACGAGGTTTC CCAGTTACAGGAAGAGCTGACAAGAATTTCTGAGACAACAGAGTTCAACA CGATGAAGCTGCTGGATGGTTCTCAGAGTGGAAGTACATCTTCAACCGGG TCAGGTCCGAAGTTTGGTGTTGTAGATGCAACATTAGACGGTGCACTTGT AACATCTAACGTGAAAGGTATTAAAGTAGCAACAGCAGCTGCCACAACAA CAAAGGCAGGTCAGGAGACTGCTATCTGGGCTGCTGATGGAAAGACATTA ACTTTAAATCTTTCGAAAAATAAGGTATATACACAGGACGAAATTGATGA CTTGATCGCAAATGCAAAACAGGAAGACAGTTCTGCAACGGGTGCACCGG CTGAAGTGAAAGTATCTTTAAAGAATGGTATTTTTAATGCAGATGCAGAC ACAACTGCCGGAACTGTAACAGCCGGTGGTGTGAAGGCAGTATCTGATGA AGGAACAGTAACTGGATTTGTTGGTGCAGATACAATTTCATTTACGGCAA ATAAGTATGGAGCAGAGTTCAATGATACTGTATTTAAATTCAAATTTGAT AAGGCAGCAGGCAAAGAAGAAGTAGAGACAAATACAGCAATTGAAATTGA TGGAGCAAATGCGGTAACAGCAGGTGAATATACAATTCATCTTGCAGCAG GCAAAGAATATACGGCAGAAGATTTAGAAGATGTTCTTAAAACGGCAGGA TTCGACTTTGATGTTAAATTAAGTGGAAATACACCAGATGAGCCAAATAC TTTATTTGCAACCAGTGGCGCATCAACTGTGACTGATATTACAATGGGTG CTGGCACCGCCGGAGCTGGTCTTGGAAGTACAGATGCTATGTGGGGGCAA GCTGGTTATGACAGTTATCTTCTGGTGCTGGCATTACCTTGCAGATTGGT GCAAATGAAGGTCAGACCATGAGTTTCTCTATCGATGACATGAGTGCAAG AGCACTTGGCGTAGATGGCAACAAAGTTGATTTAAGCACACAGGCTGGCG CACAGAAAGCAACTGATACCATTGATGCAGCAATCAAGAAAGTATCTGCA CAGCGTGGTAGAATGGGTGCGATCCAGAACCGTCTGGAGCACACCATCAG CAACCTTGATACAGCAGCAGAGAATACCCAGACTGCAGAGTCCCGTATCC GTGATACAGATATGGCAGAAGAGATGGTTGAGTACTCCAAGAACAACATT CTTGCACAGGCAGGTCAGTCTATGCTTGCACAGGCGAACCAGTCTACACA GGGTGTACTCTCCTTATTACAGTAA

In one aspect, the polynucleotide sequence encodes a Roseburia flagellin selected from the group consisting of Fla1, Fla2, Fla3 and Fla4. In one embodiment, the polynucleotide sequence encodes a Roseburia flagellin selected from the group consisting of Fla2, Fla1, Fla4 and combinations thereof. In a further embodiment, the polynucleotide sequence encodes the Roseburia flagellin Fla2.

In one aspect, the polynucleotide sequence encoding Roseburia flagellin is selected from the group consisting of a polynucleotide sequence encoding Roseburia hominis Fla1, a polynucleotide sequence encoding Roseburia hominis Fla2, a polynucleotide sequence encoding Roseburia intestinalis Fla1, a polynucleotide sequence encoding Roseburia intestinalis Fla2, a polynucleotide sequence encoding Roseburia intestinalis Fla3 and a polynucleotide sequence encoding Roseburia intestinalis Fla4. In one embodiment, the polynucleotide sequence encoding Roseburia flagellin is selected from the group consisting of a polynucleotide sequence encoding Roseburia hominis Fla2, a polynucleotide sequence encoding Roseburia intestinalis Fla2, a polynucleotide sequence encoding Roseburia intestinalis Fla1, a polynucleotide sequence encoding Roseburia intestinalis Fla4 and combinations thereof. In a further embodiment, the polynucleotide sequence encoding Roseburia flagellin is selected from the group consisting of a polynucleotide sequence encoding Roseburia hominis Fla2, a polynucleotide sequence encoding Roseburia intestinalis Fla2 and combinations thereof. In another embodiment, the polynucleotide sequence encoding Roseburia flagellin is a polynucleotide sequence encoding Roseburia intestinalis Fla2.

The therapeutic effect of flagellins were evaluated by the inventors by functional assays.

In one embodiment, the Roseburia flagellin is a truncated Roseburia flagellin. For example, the truncated Roseburia flagellin comprises at least 20, 30, 40, 50, 75, 100, 125, 150, 175 or 200 amino acids of polypeptide shown as SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12.

In one embodiment, the truncated Roseburia flagellin is a truncated Roseburia hominis flagellin or a truncated Roseburia intestinalis flagellin.

In one embodiment, the polynucleotide sequence encoding the Roseburia flagellin encodes a truncated FlaA1, Fla2, Fla3 or Fla4. For example, the polynucleotide sequence encodes a truncated Roseburia flagellin comprising at least 20, 30, 40, 50, 75, 100, 125, 150, 175 or 200 amino acids of polypeptide shown as SEQ ID NO 2, SEQ ID NO 4, SEQ ID NO 6, SEQ ID NO 8, SEQ ID NO 10 or SEQ ID NO 12.

In one embodiment, the polynucleotide sequence encoding the Roseburia flagellin encodes a truncated FlaA1 or Fla3.

In one embodiment, the Roseburia flagellin is a fusion polypeptide. For example, the polypeptide is fused to glutathione S-transferase (GST).

TABLE-US-00015  TABLE A-summary of the Roseburia flagellin sequences described herein and the bacterial strain from which they may be derived. Bacteria  Nucleotide Amino Acid and strain Abbreviation Sequence ID  Nucleotide Sequence Sequence ID  Amino Acid Sequence Roseburia hominis RhFlaA1 or SEQ. ID 1 ATGGTAGTACAGCACAATCTTACAGCAAT SEQ. ID 2 MVVQHNLTAMNANRQLGITTG A2-183(fla 1) RHFlaA1 or GAACGCTAACAGACAGTTAGGTATCACA AQAKSSEKLSSGYKINRAADDAA RhFla1 or ACAGGCGCACAGGCTAAGTCTTCTGAGA GLTISEKMRSQVRGLNKASDNAQ RHFIa1 or AGTTATCTTCTGGTTACAAGATCAACCGC DGVSLIQVAEGALSETHSILQRMN Rh1 or RH1 GCAGCAGATGACGCAGCAGGTCTTACGA ELATQAANDTNTTSDRTAVQQEI TTTCCGAGAAGATGAGAAGCCAGGTTAG NQLASEITRIASTTQFNTMNLIDG AGGCTTAAATAAAGCTTCTGACAACGCAC NFTSKKLQVGSLCGQAITIDISDM AGGATGGTGTATCCCTTATTCAGGTAGCT SATGLGVSGLVVSSFSAAGKAMS GAGGGTGCATTAAGTGAGACACACTCCA AAQDAISYVSSMRSKLGALQNRL TCTTACAGCGTATGAATGAGTTAGCAACT EHTISHLDNISEHTSSAESRIRDTD CAGGCAGCAAACGATACCAATACAACCT MAEEMVEYSKNNILAQAGQSML CAGACAGAACTGCAGTTCAGCAGGAGAT AQANQSTQGVLSLLQ CAACCAGTTAGCATCTGAGATCACCAGAA TCGCTTCTACAACTCAGTTCAACACAATG AACCTGATCGATGGTAACTTCACAAGTAA GAAGCTTCAGGTAGGTTCCCTTTGCGGAC AGGCTATCACAATCGATATCTCTGATATG TCTGCTACAGGTCTTGGCGTTAGCGGATT AGTAGTATCTTCCTTCTCTGCAGCTGGTA AGGCAATGTCTGCAGCTCAGGATGCTAT CAGCTACGTATCTTCTATGCGTTCTAAGC TGGGTGCATTACAGAACAGACTTGAGCA CACAATCTCCCACCTGGACAACATTTCTG AGCACACATCTTCTGCAGAGTCTCGTATC CGTGATACAGATATGGCTGAAGAGATGG TTGAGTACAGCAAGAACAACATCCTTGCT CAGGCAGGACAGTCTATGCTTGCTCAGG CTAACCAGTCTACTCAGGGTGTATTATCC TTATTACAGTAA Roseburia hominis RhFlaA2 or SEQ. ID 3 ATGGTGGTTAATCATAATATGGCGGCAA SEQ. ID 4 MVVNHNMAAICESRQLRYNVKK A2-183 (fla2) RHFlaA2 or TCTGTGAGAGCAGGCAGCTGCGCTATAA MEKSSKKLATGYKLNTANDDAAG RhFla2 or CGTGAAGAAGATGGAAAAATCTTCCAAA LQISETMRHHVKGLNKASRNSQD RHFIa2 or AAGCTTGCGACAGGGTACAAGCTGAACA GISMLQTADAALQETQDVLDRM Rh2 or RH2 CAGCAAATGATGATGCGGCAGGCTTGCA VELTTQAANDINTDSDRRAIQDEL GATATCAGAGACGATGCGGCATCATGTG DQLNKEVDRIAYTTHFNQQYMLA AAAGGGCTGAACAAAGCCTCCCGGAATT EGTPQAAPGYYRIQSGALNGQAI CACAGGACGGCATCAGTATGCTGCAGAC DIHFVNASKESLGTDKVNVSSHAK GGCGGATGCAGCGCTCCAAGAGACGCA ASESITMVQDAIEQAALWRDEFG GGATGTTCTCGATCGTATGGTGGAGCTG SQQERLEHAVRNTDNTSQNTQS ACGACGCAGGCAGCCAATGACATCAACA AESGIRDTNMNMEMVLYSTNRIL CAGACTCGGATCGCAGGGCTATTCAGGA VHASQSILAQYNDDAKSVLEILK TGAGTTGGATCAGCTGAACAAGGAAGTG GACCGCATCGCCTATACGACGCACTTCAA TCAGCAGTATATGTTGGCGGAGGGAACG CCGCAGGCGGCACCGGGATATTACCGCA TACAGTCCGGGGCACTGAACGGACAGGC GATAGATATCCATTTTGTAAATGCGAGCA AGGAGAGCCTTGGCACAGACAAAGTGAA TGTATCTTCGCATGCGAAGGCGTCGGAA TCCATCACGATGGTTCAGGACGCGATTG AACAGGCGGCGCTCTGGAGAGACGAGTT CGGCAGCCAGCAGGAGCGTCTGGAACAT GCCGTGCGCAATACGGACAACACATCAC AAAATACGCAGAGTGCGGAGTCAGGGAT CAGAGACACCAACATGAATATGGAGATG GTATTATATTCGACCAACCGGATTCTGGT GCATGCATCCCAGAGTATTCTGGCACAGT ATAATGATGATGCAAAATCAGTGCTTGA GATTTTGAAATAG Roseburia RiFlaA1 or SEQ. ID 5 ATGCGTGGCGGAGACAATAGAAGGAGA SEQ. ID 6 MRINYNVSAAIANKHLLGIEDNLS intestinalis  RIFIaA1 AACAGAATGAGAATTAATTACAATGTGTC ASMERLSSGLKINHSKDNPAGMA L1-82 (fla1) RiFla1 or AGCAGCGATTGCGAATAAACATTTACTTG ISNKMKAQIDGLNRASQNASDGI RIFla1 or Ri1 GAATTGAGGATAATTTAAGTGCATCGAT SVIQIADGALSETTSILQRMRELSV or RI1 GGAACGGCTTTCATCGGGACTTAAGATC QAASDATMTPADKEAIQKEITSLK AACCATTCCAAGGACAATCCGGCAGGAA DEVDRISTDTEYNSKTLLDGSLDT TGGCTATTTCCAACAAGATGAAAGCACA RVYTKNATRVDISDHVKAGQYQL GATTGATGGTTTAAACCGGGCTTCCCAGA SIDTAATQAGPVTANQNYNSTAP ATGCATCGGATGGTATTTCTGTTATTCAG VGASGTMSINGSKVEIEAADTYAE ATCGCAGATGGTGCGCTGAGTGAAACGA AFEKIRNAAETGETTVKIEKNGALS CCAGTATTTTACAGCGTATGAGAGAACTT FTAEQYGMSSILEIAFDDKQLANA TCCGTGCAGGCAGCGAGTGATGCAACAA LGFTADGGNSVVEDPENKGSYVY TGACACCGGCGGATAAAGAAGCAATCCA GQIQNGKVIVPSGTDAEVTLTKPS GAAAGAAATCACTTCATTAAAAGATGAA DGTGFGDTATVKTDGNKITVTDR GTTGACCGTATTTCTACAGATACAGAGTA AGFEMSFLADAGYTGKLDFDVTD TAACAGCAAAACACTTTTAGATGGTTCAT IGTMALHIGANEDQETRVRIPEVS TAGATACCAGGGTTTACACCAAAAATGCA CKSLYIDDADVTTVNGAGRGITQF ACAAGAGTGGACATTTCTGATCATGTGA DDAISKVSEVRSRLGAYQNRLEST AAGCAGGACAGTATCAGCTTTCCATTGAT VSSLDTFEENMTGAQSRLTDAD ACTGCAGCTACACAGGCCGGACCGGTAA MASEMTDYTHQNVLNQAAISVL CAGCAAATCAGAATTATAATTCCACAGCA TQANDLPQ CCGGTCGGTGCGTCCGGAACAATGAGTA TTAATGGTTCTAAAGTAGAGATAGAGGC AGCCGACACCTATGCGGAGGCTTTTGAG AAGATCAGAAATGCAGCAGAGACTGGTG AAACAACCGTTAAGATTGAAAAGAATGG AGCACTTTCATTTACCGCAGAACAGTACG GAATGTCAAGCATCTTAGAGATCGCATTN NTGATGATAAGCAGCTTGCTAATGCACTT GGATTTACAGCAGACGGAGGAAACAGTG TTGTAGAAGATCCAGAGAATAAAGGCAG CTATGTATACGGACAGATTCAGAATGGC AAAGTGATCGTACCTTCCGGTACAGATGC CGAAGTAACGCTCACAAAACCGAGTGAT GGAACCGGATTTGGTGATACAGCTACGG TAAAAACAGATGGAAATAAGATTACGGT TACAGACAGAGCCGGATTTGAGATGTCA TTTCTTGCTGATGCAGGTTATACGGGTAA GCTGGATTTTGATGTCACGGATATCGGA ACGATGGCACTTCATATTGGAGCAAATG AGGATCAGGAAACAAGAGTGCGTATTCC GGAGGTTTCCTGCAAGAGCCTTTACATTG ATGATGCAGACGTGACGACTGTAAATGG AGCAGGCAGAGGTATCACACAGTTTGAC GATGCCATTTCAAAGGTCAGTGAAGTGC GTTCAAGACTTGGTGCATACCAGAATCGT CTTGAGAGTACGGTATCAAGCCTGGATA CGTTTGAAGAAAATATGACAGGAGCCCA GTCACGACTGACAGATGCGGATATGGCA TCGGAAATGACAGATTATACACATCAGA ATGTATTAAATCAGGCAGCAATCTCTGTT TTGACACAGGCAAACGATCTGCCACAGC AGGTATTGCAGATTCTGCAGTAA Roseburia RiFla2 or SEQ. ID 7 ATGGTAGTTAATCATAATATGGCATTGAT SEQ. ID 8 MVVNHNMALICESRQLRCNVKN intestinalis  RIFIa2 or Ri2 CTGTGAGAGTAGACAGTTACGATGTAAT MEKSSKKLATGYKLLGANDDAAG L1-82 (fla2) or RI2 GTGAAGAACATGGAGAAGTCTTCAAAAA LQISETMRHQTRGLNKASRNSQD AGCTGGCAACAGGTTATAAATTGCTTGG GISMLQTADAALQETQEVLDRM AGCAAATGATGATGCAGCAGGATTACAG TDLTTQAANDINTDADRRAIQDEI ATATCAGAAACCATGCGTCATCAGACCAG DQLNQEVDRIAYTTNFNQQYILA AGGTCTTAACAAAGCATCCAGAAATTCGC DGTPQARPGYYMIQTGSLAGQGI AAGATGGAATTAGTATGCTGCAGACAGC EIKFVNASKESLGVDKVDVSSHAK AGATGCAGCATTACAGGAGACACAGGAA ATESIAVVQNAIEKAASFRDTFGA GTGTTGGATCGAATGACGGATCTGACAA QQERLEHALRGTDNTSESTQRAE CACAGGCAGCTAATGATATCAATACGGA SSRRDTNMNMEMVQYSTNRILV TGCGGATCGTCGTGCAATTCAGGATGAA QASQSILAQYNDDAKYVLEMLKQ ATCGATCAGTTAAATCAGGAAGTGGATC VLQILQ GTATTGCATATACGACGAATTTTAATCAG CAGTATATATTAGCGGATGGAACTCCGC AGGCAAGACCAGGATACTATATGATACA GACAGGAAGTCTTGCGGGACAGGGAATA GAGATTAAGTTTGTTAATGCGAGCAAAG AGAGCTTGGGTGTGGACAAGGTTGATGT ATCATCGCATGCAAAAGCGACAGAATCT ATAGCAGTGGTACAGAATGCAATTGAAA AGGCAGCTTCGTTTAGAGATACATTTGG GGCACAACAGGAGCGGTTAGAACACGCA TTGCGTGGAACGGATAATACATCAGAAA GTACACAGAGGGCAGAATCAAGTAGACG CGATACCAACATGAATATGGAGATGGTA CAATATTCTACAAACCGTATTTTAGTACA GGCATCTCAGAGTATTTTAGCACAGTACA ATGATGATGCAAAATATGTGTTGGAAAT GTTAAAATAG Roseburia RiFla3 or SEQ. ID 9 ATGGTAGTACAGCACAATATGACCGCAA SEQ. ID 10 MVVQHNMTAMNANRMLGVTT intestinalis  RIFla3 or Ri3 TGAATGCGAACAGAATGTTAGGCGTTAC SAQAKSSEKLSSGYRINRAGDDAA L1-82 (fla 3) or RI3 AACAAGCGCACAGGCAAAATCTTCAGAG GLTISEKMRSQIRGLNKASDNAQ AAATTATCTTCTGGTTACAGAATCAACCG DGISLIQVAEGALSETHSILQRMN TGCAGGTGATGACGCTGCTGGTTTAACA ELATQAANDTNTTADRGAIQDEI ATTTCTGAGAAGATGAGAAGCCAGATCC NQLTSEINRISSTTQFNTQNLIDGT GTGGATTAAACAAAGCTTCTGACAACGC FANKNLQVGSICGQRITVSIDSMS ACAGGATGGTATTTCCTTAATCCAGGTTG AGSLNVSANLVKVNTFSAAGEA CTGAGGGTGCATTATCTGAGACACATTCT MSNIQGAISAISTQRSYLGALQNR ATCTTACAGCGTATGAATGAGTTAGCTAC LEHTISNLDNISENTQSAESRIRDT TCAGGCTGCTAACGATACCAATACAACTG DMAEEMVTYSKNNILAQAGQSM CTGATAGAGGAGCTATTCAGGATGAGAT LAQANQSTQGVLSLLQ CAACCAGTTAACATCTGAGATTAACAGAA TCTCTTCTACAACTCAGTTCAATACTCAGA ACCTCATCGATGGTACATTCGCAAATAAA AACCTTCAGGTTGGTTCTATCTGTGGACA GAGAATTACTGTTTCTATCGACAGTATGT CTGCTGGTAGCTTAAATGTATCTGCTAAC TTAGTAAAGGTTAACACTTTCAGTGCAGC AGGTGAAGCAATGTCCAATATTCAGGGT GCTATTTCTGCAATTTCTACACAGCGTTCT TACTTAGGAGCTCTTCAGAATCGTCTGGA GCATACAATCTCCAACTTGGACAACATTT CTGAGAATACTCAGTCTGCTGAATCTCGT ATCCGTGATACAGATATGGCTGAAGAGA TGGTTACTTACAGCAAGAACAATATTCTT GCTCAGGCAGGACAGTCTATGCTTGCTCA GGCTAACCAGTCTACTCAGGGTGTACTTT CTCTGTTACAGTAA Roseburia RiFla4 or SEQ. ID 11 ATGGCAATGGTAGTACAGCACAACATGT SEQ. ID 12 MAMVVQHNMSAMNANRNLGV intestinalis  RIFIa4 or Ri4 CCGCAATGAATGCGAACAGAAATTTAGG TTGMQAKSSEKLSSGYKINRAAD L1-82 (fla4) or RI4 TGTTACAACAGGAATGCAGGCAAAATCA DAAGLSISEKMRSQIRGLNKASD TCAGAGAAGTTATCTTCCGGTTACAAGAT NAQDGISLIQTAEGALNESHSILQ CAACCGTGCAGCAGATGATGCAGCAGGA RMRELSVQAANGTETDDDREAV CTTTCTATTTCTGAGAAGATGAGAAGCCA QNEVSQLQEELTRISETTEFNTMK GATCCGCGGTTTAAATAAAGCATCTGACA LLDGSQSGSTSSTGSGPKFGVVD ATGCACAGGATGGTATCTCTTTAATCCAG ATLDGALVTSNVKGIKVATAAATT ACCGCTGAGGGAGCATTAAATGAGTCCC TKAGQETAIWAADGKTLTLNLSK ACTCTATTTTACAGAGAATGAGAGAGTTA NKVYTQDEIDDLIANAKQEDSSAT TCCGTACAGGCAGCCAACGGTACAGAGA GAPAEVKVSLKNGIFNADADTTA CAGATGACGACCGCGAGGCAGTACAGAA GTVTAGGVKAVSDEGTVTGFVG CGAGGTTTCCCAGTTACAGGAAGAGCTG ADTISFTANKYGAEFNDTVFKFKF ACAAGAATTTCTGAGACAACAGAGTTCA DKAAGKEEVETNTAIEIDGANAVT ACACGATGAAGCTGCTGGATGGTTCTCA AGEYTIHLAAGKEYTAEDLEDVLK GAGTGGAAGTACATCTTCAACCGGGTCA TAGFDFDVKLSGNTPDEPNTLFAT GGTCCGAAGTTTGGTGTTGTAGATGCAA SGASTVTDITMGAGTAGAGLGST CATTAGACGGTGCACTTGTAACATCTAAC DAMWGQAGYDSVSSGAGITLQI GTGAAAGGTATTAAAGTAGCAACAGCAG GANEGQTMSFSIDDMSARALGV CTGCCACAACAACAAAGGCAGGTCAGGA DGNKVDLSTQAGAQKATDTIDAA GACTGCTATCTGGGCTGCTGATGGAAAG IKKVSAQRGRMGAIQNRLEHTIS ACATTAACTTTAAATCTTTCGAAAAATAA NLDTAAENTQTAESRIRDTDMAE GGTATATACACAGGACGAAATTGATGAC EMVEYSKNNILAQAGQSMLAQA TTGATCGCAAATGCAAAACAGGAAGACA   NQSTQGVLSLLQ GTTCTGCAACGGGTGCACCGGCTGAAGT GAAAGTATCTTTAAAGAATGGTATTTTTA ATGCAGATGCAGACACAACTGCCGGAAC TGTAACAGCCGGTGGTGTGAAGGCAGTA TCTGATGAAGGAACAGTAACTGGATTTG TTGGTGCAGATACAATTTCATTTACGGCA AATAAGTATGGAGCAGAGTTCAATGATA CTGTATTTAAATTCAAATTTGATAAGGCA GCAGGCAAAGAAGAAGTAGAGACAAAT ACAGCAATTGAAATTGATGGAGCAAATG CGGTAACAGCAGGTGAATATACAATTCAT CTTGCAGCAGGCAAAGAATATACGGCAG AAGATTTAGAAGATGTTCTTAAAACGGCA GGATTCGACTTTGATGTTAAATTAAGTGG AAATACACCAGATGAGCCAAATACTTTAT TTGCAACCAGTGGCGCATCAACTGTGACT GATATTACAATGGGTGCTGGCACCGCCG GAGCTGGTCTTGGAAGTACAGATGCTAT GTGGGGGCAAGCTGGTTATGACAGTTAT CTTCTGGTGCTGGCATTACCTTGCAGATT GGTGCAAATGAAGGTCAGACCATGAGTT TCTCTATCGATGACATGAGTGCAAGAGC ACTTGGCGTAGATGGCAACAAAGTTGAT TTAAGCACACAGGCTGGCGCACAGAAAG CAACTGATACCATTGATGCAGCAATCAAG AAAGTATCTGCACAGCGTGGTAGAATGG GTGCGATCCAGAACCGTCTGGAGCACAC CATCAGCAACCTTGATACAGCAGCAGAG AATACCCAGACTGCAGAGTCCCGTATCCG TGATACAGATATGGCAGAAGAGATGGTT GAGTACTCCAAGAACAACATTCTTGCACA GGCAGGTCAGTCTATGCTTGCACAGGCG AACCAGTCTACACAGGGTGTACTCTCCTT ATTACAGTAA

TABLE-US-00016 Table B - summary of the accession numbers for Roseburia flagellins described herein. Protein Accession Genome or Gene Protein Accession Number Accession Number (NCBI Reference Bacteria and strain Abbreviation Number (GenBank) Sequence) Roseburia hominis A2- RhFlaA1 or RHFlaA1 or DQ789140.1 ABI48297.1 ABI48297.1 183(fla 1) RhFla1 or RHFla1 or Rh1 or RH1 Roseburia hominis A2-183 RhFlaA2 or RHFlaA2 or DQ789141.1 ABI48298.1 ABI48298.1 (fla 2) RhFla2 or RHFla2 or Rh2 or RH2 Roseburia intestinalis L1- RiFlaA1 or RIFlaA1 RiFla1 or ABYJ02000009.1 EEV02820 WP_006855378 82 (fla1) RIFla1 or Ri1 or RI1 Roseburia intestinalis L1- RiFla2 or RIFIa2 or Ri2 or ABYJ02000032.1 EEV02466 WP_006855745 82 (fla2) RI2 Roseburia intestinalis L1- RiFla3 or RIFla3 or Ri3 or ABYJ02000104.1 EEV00779 WP_006857364 82 (fla3) RI3 Roseburia intestinalis L1- RiFla4 or RIFla4 or Ri4 or ABYJ02000202.1 EEU99488 WP_006858703 82 (fla4) RI4

Modulation/Regulation

The terms “modulation” and “regulation” may be used interchangeably herein.

In one embodiment, the term “modulation” refers to an increase and/or induction and/or promotion and/or activation. In an alternative embodiment, the term “modulation” refers to a decrease and/or reduction and/or inhibition.

In one embodiment, the term “regulation” refers to an upregulation. In an alternative embodiment, the term “regulation” refers to a downregulation.

In one embodiment, the Roseburia flagellin, and/or Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), reduces the inflammation of a tissue or an organ.

For example, inflammation of the alimentary canal or part thereof (such as the intestine) is reduced.

The term “inflammation” as used herein refers to one or more of the following: redness, swelling, pain, tenderness, heat, and disturbed function of a tissue or organ due to an inflammatory process triggered by over-reaction of the immune system.

A reduction in inflammation in a subject can be determined by determining the levels of pro-inflammatory cytokines and chemokines in tissue, serum and/or faecal samples in a subject before, and after, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the levels of one or more of the following can be monitored: IL-1, IL-4, IL5, IL6, IL-8, IL-12, IL-13, IL-17, IL-21, IL-22, IL23, TNFα, IFNγ, CXCL1, CXCL10, CCL2, CCL20 serum and faecal calprotectin, SA1009/SA1008 calcium binding proteins, and Type 1 interferons, CD markers such as CD163, CD14, inflammatory transcription factors such as NF-kB, STAT, and MAPkinases, c-reactive protein (CRP), erythrocyte sedimentation rate (ESR), complement proteins, serum albumin, histological evaluation of target tissues and organs, disease activity indices. Further, in human studies quality of life (QoL) questionnaires can be carried out before, and after, the Roseburia flagellin, and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the amount of a tissue or organ which is inflamed in a subject is at least 10%, 20%, 30%, 40% or 50% lower when compared to the amount of tissue or organ which is inflamed in a subject before the Roseburia flagellin, and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the Roseburia flagellin, and/or Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), reduces the inflammation by epithelial cells of the tissue or the organ.

For example, the epithelial cells are epithelial cells of the alimentary canal or part thereof (such as the intestine).

In one embodiment, the Roseburia flagellin, and/or Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), increases the production of T cells in a subject.

In one embodiment, the T cells are regulatory T cells (also referred to as Tregs) such as regulatory T cells capable of expressing TLR5 (Toll-like receptor 5).

Without wishing to be bound by theory, an increase in Treg numbers will combat the effects of other effector T cells (also referred to as Teffs), such as Th1, Th17 and Th2 which drive inflammation, autoimmunity and allergic/atopic conditions. Hence this property of the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), can be exploited to address many diseases where Teff/Treg cell balance is lost, e.g. Crohn's and ulcerative colitis.

In one embodiment, the production of T cells in a subject is increased such that there are at least 10%, 20%, 30%, 40% or 50% more T cells, or greater than 100% more T cells, when compared to the number of T cells in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “immune system” as used herein may refer to the adaptive immune system and/or the innate immune system.

In one aspect, the invention relates to the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating the adaptive immune system of a subject.

As used herein, the term “adaptive immune system”, otherwise known as the “specific immune system” refers to highly specialized, systemic cells and processes that eliminate or prevent pathogenic growth. The adaptive immune response provides the vertebrate immune system with the ability to recognize and remember specific pathogens (to generate immunity), and to mount stronger attacks each time the pathogen is encountered.

As used herein, the term “regulating the adaptive immune system” means inducing the activity of the adaptive immune system, and/or promoting immune homeostatic mechanisms by increasing the level of activity relative to the baseline level of activity. Preferably, the adaptive immune system is modulated towards immune regulation (and not immune activation therefore reducing inflammation).

Defects and disorders associated with the adaptive immune system, particularly related to the function of T cells, are associated with many inflammatory and autoimmune diseases. T cell responses associated with Th1, Th2 and Th17 are associated with atopic, inflammatory and autoimmune diseases. Therapies which improve or increase T regulatory (Tregs) cell populations are important in controlling diseases driven by excessive Th1, Th2 and Th17 cell responses.

Another aspect of the invention relates to the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in regulating the innate immune system of a subject.

As used herein, the term “innate immune system”, also known as the non-specific immune system, comprises the cells and mechanisms that provide the host with immediate defense against infection by other organisms in a non-specific manner. This means that the cells of the innate system recognize and respond to pathogens in a generic way, but unlike the adaptive immune system, it does not confer long-lasting or protective immunity to the host.

As used herein, the term “regulating the innate immune system” means inducing the activity of the innate immune system, and/or increasing the level of activity relative to the baseline level of activity such that it promotes immune homeostasis.

Loss or dysregulation of the innate immune function, either due to loss of epithelial barrier, innate immune peptides such as defensins, chemokines and cytokines or defective TLR signalling are associated with increased risk of inflammatory diseases, in several body organs including the gut. Such diseases include inflammatory bowel disease.

In one embodiment, the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), restores immunological tolerance.

As used herein, the term “immunological tolerance” refers to the process by which the immune system does not attack an antigen such as a self-antigen.

As used herein the term “restoring immunological tolerance” refers to a restoration in immunological tolerance to one or more antigens (such as a self-antigen) in a subject such that the level of immunological tolerance to the antigen is higher when compared to the levels in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), activates dendritic cells and/or epithelial cells.

As used herein the term “activates dendritic cells” refers to an up-regulation of one or more cells markers (such as I-A/I-E cell markers, CD80 and CD86 and CD40) and/or an increase in the production of one or more cytokines (such as IL-10 and TGF□) by cells (such as dendritic cells) in a subject when compared to the levels in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “I-A/I-E” as used herein refers to cell markers of MHC class II.

CD40 has an essential role in immunity, and is one of the best characterized of the costimulatory molecules. This receptor, a member of the tumor necrosis factor receptor family, is expressed by professional antigen-presenting cells, such as dendritic cells. CD40 binds its ligand CD40L, which is transiently expressed on T cells and other non-immune cells under inflammatory conditions.

CD40L is an example of a T cell marker. CD3, CD4, CD25, FoxP3, CTLA-4, Ly6 g and CD11b are further examples of T cell markers.

CD80 and CD86 are expressed on antigen-presenting cells (such as dendritic cells) and are required for the development and costimulation of T cell responses. The CD28 and CTLA-4 molecules on T cells serve as receptors for the CD80 and CD86 costimulatory antigens.

CD3, CD4, CD25, FoxP3, CTLA-4, Ly6 g and CD11b are examples of markers of colonic T regulatory cells.

Without wishing to be bound by theory, the depletion of Ly6 g (e.g. Ly6 g6c and ly6 g6e) increases infection risk, both gut and respiratory tract and is associated with diseases such as neutropenia. Thus, in one embodiment, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is for use in treating neutropenia.

Another aspect of the invention relates to the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), for use in maintaining immune homeostasis in a subject. As used herein “maintaining immune homeostasis” refers to the self-regulation of the body's immune system to maintain oral tolerance or immune stability in response to changing conditions. Oral tolerance refers to the normal immune responses to food and commensal bacteria in a healthy gut. These are lost in coeliac disease and Inflammatory Bowel Diseases such as Crohn's disease and ulcerative colitis. Thus, in one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is for use in treating coeliac disease and Inflammatory Bowel Diseases such as Crohn's disease and ulcerative colitis.

In one embodiment, the numbers of a cell marker on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of the cell marker on the cell(s), or greater than 100% more of the cell marker on the cell(s), when compared to the number of the cell marker on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have the cell marker are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have the cell marker, or greater than 100% more cells which have the cell marker, when compared to the number of cell with the cell marker in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one aspect, the cells are T cells.

In another aspect, the cells are cells of the alimentary canal (such as cells of the intestine).

In a further aspect, the cells are colonic and/or small intestinal T regulatory cells and may be either CD4 or CD8 positive.

In one aspect, the cell marker is a T cell marker. In another aspect, the cells marker is a colonic T cell marker.

Markers which are type I-A/I-E are examples of a cell marker. CD40 is another example of a cell marker both found on dendritic cells.

In one embodiment, the level of a cytokine in a subject is increased such that the cytokine level is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the cytokine level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

Examples of dendritic cells include bone marrow dendritic cells and gut mucosal dendritic cells.

As used herein the term “activates epithelial cells” refers to an increase in the expression of one or more pro-inflammatory genes by epithelial cells in a subject when compared to the expression levels in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “pro-inflammatory gene” as used herein refers to a gene which, when expressed, promotes inflammation. Examples of pro-inflammatory genes include genes encoding but not limited to IL1-β, IL4, IL5, IL6, IL8, IL12, IL13, IL17, IL21, IL22, IL23, IL27, IFNγ, CCL2, CCL3, CCL5, CCL20, CXCL5, CXCL10, CXCL12, CXCL13, and TNF-α.

In one embodiment, the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), upregulates the production of a cytokine.

The term “upregulates the production of a cytokine” as used herein refers to an increase in the level of a cytokine in a subject compared to the level of the cytokine in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the level of the cytokine is increased such that the level is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In another embodiment, the Roseburia flagellin, and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), upregulates the production of IL-10 and/or TGF□.

The term “upregulates the production of IL-10” as used herein refers to an increase in the level of IL-10 in a subject compared to the level of IL-10 in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the level of IL-10 is increased such that the level is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In some aspects, IL-10 is produced by dendritic cells such as bone marrow derived dendritic cells and gut mucosal dendritic cells in particular CD103+ subsets.

In one embodiment, the Roseburia flagellin, and/or the Fla polypeptide, and/or the polynucleotide sequence encoding the Roseburia flagellin and/or the Fla (such as FlaA1 or FlaA2) polypeptide, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), upregulates the production cell surface markers involved in immune responses and antigen recognition in a cell or cells of a subject.

Examples of cell surface markers involved in immune responses and antigen recognition include CD40, I-A/I-E, CD317/BST-2, CD103, CD80, CD86, CD83 and/or Siglec-H and/or the species equivalent.

Cell surface markers (e.g. CD317/BST-2) may be referred by different names in different species or the cell surface marker may not yet have been identified on the cells of a particular species. The term “species equivalent” as used herein encompasses these cell surface markers.

The term “upregulates the production CD40” as used herein refers to an increase in the level of CD40 in a subject compared to the level of CD40 in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing the cell marker CD40 is increased and/or the number of CD40 markers on a cell is increased.

In one embodiment, the numbers of the CD40 cell marker on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of the cell marker on the cell(s), or greater than 100% more of the cell marker on the cell(s), when compared to the number of the cell marker on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have the cell marker CD40 are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have the cell marker, or greater than 100% more cells which have the cell marker, when compared to the number of cell with the cell marker in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production I-A/I-E” as used herein refers to an increase in the level of I-A/I-E in a subject compared to the level of I-A/I-E in a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more I-A/I-E cell markers is increased and/or the number of I-A/I-E cell markers on a cell is increased.

In one embodiment, the numbers of the I-A/I-E cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of I-A/I-E cell markers on the cell(s), or greater than 100% more of I-A/I-E cell markers on the cell(s), when compared to the number of I-A/I-E cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have I-A/I-E cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have I-A/I-E cell markers, or greater than 100% more cells which have I-A/I-E cell markers, when compared to the number of cell with I-A/I-E cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of CD317/BST-2” as used herein refers to an increase in the level of CD317/BST-2 in a subject compared to the level of CD317/BST-2 in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more CD317/BST-2 cell markers is increased and/or the number of CD317/BST-2 cell markers on a cell is increased.

In one embodiment, the numbers of the CD317/BST-2 cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of CD317/BST-2 cell markers on the cell(s), or greater than 100% more of CD317/BST-2 cell markers on the cell(s), when compared to the number of CD317/BST-2 cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have CD317/BST-2 cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have CD317/BST-2 cell markers, or greater than 100% more cells which have CD317/BST-2 cell markers, when compared to the number of cell with CD317/BST-2 cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of CD103” as used herein refers to an increase in the level of CD103 in a subject compared to the level of CD103 in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more CD103 cell markers is increased and/or the number of CD103 cell markers on a cell is increased.

In one embodiment, the numbers of the CD103 cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of CD103 cell markers on the cell(s), or greater than 100% more of CD103 cell markers on the cell(s), when compared to the number of CD103 cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have CD103 cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have CD103 cell markers, or greater than 100% more cells which have CD103 cell markers, when compared to the number of cell with CD103 cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of CD80” as used herein refers to an increase in the level of CD80 in a subject compared to the level of CD80 in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more CD80 cell markers is increased and/or the number of CD80 cell markers on a cell is increased.

In one embodiment, the numbers of the CD80 cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of CD80 cell markers on the cell(s), or greater than 100% more of CD80 cell markers on the cell(s), when compared to the number of CD80 cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have CD80 cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have CD80 cell markers, or greater than 100% more cells which have CD80 cell markers, when compared to the number of cell with CD80 cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of CD86” as used herein refers to an increase in the level of CD86 in a subject compared to the level of CD86 in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more CD86 cell markers is increased and/or the number of CD86 cell markers on a cell is increased.

In one embodiment, the numbers of the CD86 cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of CD86 cell markers on the cell(s), or greater than 100% more of CD86 cell markers on the cell(s), when compared to the number of CD86 cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have CD86 cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have CD86 cell markers, or greater than 100% more cells which have CD86 cell markers, when compared to the number of cell with CD86 cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of CD83” as used herein refers to an increase in the level of CD83 in a subject compared to the level of CD83 in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more CD83 cell markers is increased and/or the number of CD83 cell markers on a cell is increased.

In one embodiment, the numbers of the CD83 cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of CD83 cell markers on the cell(s), or greater than 100% more of CD83 cell markers on the cell(s), when compared to the number of CD83 cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have CD83 cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have CD83 cell markers, or greater than 100% more cells which have CD83 cell markers, when compared to the number of cell with CD83 cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “upregulates the production of Siglec-H” as used herein refers to an increase in the level of Siglec-H in a subject compared to the level of Siglec-H in a subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. For example, the number of cells bearing one or more Siglec-H cell markers is increased and/or the number of Siglec-H cell markers on a cell is increased.

In one embodiment, the numbers of the Siglec-H cell markers on the cell(s) of a subject are up-regulated such that there are at least 10%, 20%, 30%, 40% or 50% more of Siglec-H cell markers on the cell(s), or greater than 100% more of Siglec-H cell markers on the cell(s), when compared to the number of Siglec-H cell markers on the cell(s) of the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition or alternatively, the number of cells in a subject which have Siglec-H cell markers are increased such that there are at least 10%, 20%, 30%, 40% or 50% more cells which have Siglec-H cell markers, or greater than 100% more cells which have Siglec-H cell markers, when compared to the number of cell with Siglec-H cell markers in the subject before the Roseburia flagellin, and/or the polypeptide Fla, and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said Fla, and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In some aspects, the production of CD40 I-A/I-E, CD317/BST-2, CD80, CD86, CD83 and/or Siglec-H is by dendritic cells (such as tolerogenic CD103⁺ dendritic cells expanded by FLT3L.).

In one embodiment, the expression of one or more Type I IFN genes in a cell or cells of a subject is downregulated.

In one embodiment, the expression level of one or more Type I IFN genes is decreased such that the level is at least 10%, 20%, 30%, 40% or 50% lower when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

Examples of Type I IFN genes include but not limited to IFN-β1, IFN-β3, Lfi202b, Ifi203, IFI44, IFTI, MXI, OASI, OAS2, OAS3, OASL, Irf3 and Irf4.

In one embodiment, the expression of one or more pro-inflammatory genes in a cell or cells of a subject is downregulated.

In one embodiment, the expression level of one or more pro-inflammatory genes is decreased such that the level is at least 10%, 20%, 30%, 40% or 50% lower when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “intestinal microbiota” as used herein refers to microorganisms that live in the digestive tract of the host animals. These microorganisms perform a wide variety of metabolic, structural, protective and other beneficiary functions.

As used herein, the term “improving intestinal microbiota” refers to increasing the number and/or type of microorganisms present in the intestine of a subject (e.g. the host), and/or increasing the activity of said microorganisms in terms of their metabolic, structural, protective and other beneficiary functions. For example, the numbers (i.e. levels) of Clostridium cluster XIVa bacteria are increased and the numbers of E. coli are reduced; such an improvement in intestinal microbiota may occur in subjects with inflammatory bowel disease (IBD) once the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), has been administered to the subject.

In one embodiment, the number of microorganisms present in the intestine of a subject (e.g. the host), is increased such that the number of microorganisms is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition, or alternatively, the types of microorganisms present in the intestine of a subject (e.g. the host), are increased such that there are at least 5%, 10%, or 15% more types of microorganisms when compared to the types in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

As used herein, the term “regulating appetite” refers to the ability to modulate (i.e. increase or decrease) the desire for a subject to eat food.

In one embodiment, the appetite in the subject is stimulated (i.e. increased).

Without wishing to be bound by theory, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), exerts a stimulatory effect on the appetite of a subject by downregulating the expression of genes associated with the suppression of appetite (such as genes encoding satiety hormones). Agt, Cartpt, Cck, Cxcl12 and Gcg are examples of genes associated with regulating appetite and the downregulation of one or more of these genes is associated with the suppression of appetite.

Cck and Gcg are Examples of Satiety Hormones.

In one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), stimulates the appetite in the subject such that the subject consumes at least 5%, 10%, or 15% more food when compared to the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject. In addition, or alternatively, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), stimulates the appetite in the subject such that after 1 month from administration the weight of the subject is at least 2%, 5%, or 10% higher when compared to the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), reduces the level of cholecystokinin (Cck) and/or glucagon (Gcg) in the blood of a subject.

In one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), reduces the level of cholecystokinin (Cck) and/or glucagon (Gcg) in the blood of a subject by at least 5%, 10%, 15% or 20% when compared to the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), downregulates the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject.

In one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), decreases the expression of the gene encoding cholecystokinin (Cck) such that the expression level is at least 5%, 10%, 15% or 20% lower when compared to the expression level in the subject before the Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2) and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2) and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), decreases the expression of the gene encoding glucagon (Gcg) such that the expression level is at least 5%, 10%, 15% or 20% lower when compared to the expression level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

The term “improving alimentary canal health” as used herein refers to reducing the level of inflammation in the alimentary canal or part thereof and/or improving intestinal microbiota.

In one embodiment, the level of inflammation in the alimentary canal is at least 10%, 20%, 30%, 40% or 50% lower when compared to the level of inflammation in the alimentary canal of a subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), regulates the expression of at least one gene selected from Tlr5, Tlr1, Vnn1, Defb37, Pla2 g, Muc16, ltln, Sprr1a, Cldn4, Pmp22, Crb3, Magi3, Marveld3, Mpp7, Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a. Many of these genes are gut barrier genes and antimicrobials and hence work to reduce invasiveness of gut pathogens and also reduce the numbers of viable pathogens.

In one embodiment, the expression of one or more genes selected from the group consisting of TLR-related genes (e.g. Tlr5, Tlr1, and Vnn1), genes encoding anti-microbial peptides (e.g. Defb37, Pla2 g, Muc16, and ltln), gut barrier function genes (e.g. Sprr1a, Cldn4, Pmp22, Crb3, and Magi3), innate immune genes (e.g. Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a) in a cell or cells of a subject is upregulated.

In one embodiment, the expression of one or more genes selected from the group consisting of TLR-related genes (e.g. Tlr5, Tlr1, and Vnn1), genes encoding anti-microbial peptides (e.g. Defb37, Pla2 g, Muc16, and ltln), gut barrier function genes (e.g. Sprr1a, Cldn4, Pmp22, Crb3, and Magi3), innate immune genes (e.g. Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a) is increased such that the level is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the expression of one or more genes selected from the group consisting of Tlr5, Tlr1, Vnn1, Defb37, Pla2 g, Muc16, ltln, Sprr1a, Cldn4, Pmp22, Crb3, Magi3, Marveld3, Mpp7, Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a in a cell or cells of a subject is upregulated.

In one embodiment, the expression level of one or more genes selected from the group consisting of Tlr5, Tlr1, Vnn1, Defb37, Pla2 g, Muc16, ltln, Sprr1a, Cldn4, Pmp22, Crb3, Magi3, Marveld3, Mpp7, Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a is increased such that the level is at least 10%, 20%, 30%, 40% or 50% higher, or greater than 100% higher, when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In one embodiment, the expression of one or more genes selected from the group consisting of genes encoding acetyl-CoA acetyltransferase, 3-hydroxyacyl-CoA dehydrogenase, butyryl-CoA dehydrogenase and phosphoenolpyruvate carboxykinase [ATP] in a cell or cells of a subject is modulated.

In one embodiment, the expression level of one or more genes selected from the group consisting of genes encoding acetyl-CoA acetyltransferase, 3-hydroxyacyl-CoA dehydrogenase, butyryl-CoA dehydrogenase and phosphoenolpyruvate carboxykinase [ATP] is modulated such that the level is at least 10%, 20%, 30%, 40% or 50% higher or lower when compared to the level in the subject before the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is administered to the subject.

In a further aspect, the present invention relates to a transformed microorganism (such as a Firmicutes e.g. a Roseburia spp such as R. hominis or R. intestinalis) in which the expression of a flagellin (e.g. Roseburia flagellin) such as FlaA1 or FlaA2 is enhanced compared to the equivalent microorganism prior to transformation, and uses thereof for various therapeutic and nutritional uses as described herein. For example, the transformed microorganism may have been transformed with a nucleotide sequence (such as a promoter) such that the microorganism is capable of upregulating the expression of the gene encoding a flagellin (e.g. Roseburia flagellin) such as FlaA1 or FlaA2. In another example, the transformed microorganism may have be transformed with an expression vector comprising a nucleotide sequence encoding a flagellin (e.g. Roseburia flagellin) such as FlaA1 or FlaA2 operably linked to a regulatory sequence (such as a promoter) such that the microorganism is capable of overexpressing the gene encoding the flagellin (e.g. Roseburia flagellin) such as FlaA1 or FlaA2.

As used herein, the term “expression vector” refers to a DNA construct containing a DNA coding sequence (e.g., gene sequence) that is operably linked to one or more suitable control sequence(s) capable of affecting expression of the coding sequence in a host. Such control sequences include a promoter to effect transcription, an optional operator sequence to control such transcription, a sequence encoding suitable mRNA ribosome binding sites, and sequences which control termination of transcription and translation. The vector may be a plasmid, a phage particle, or simply a potential genomic insert. Once transformed into a suitable host, the vector may replicate and function independently of the host genome, or may, in some instances, integrate into the genome itself. The plasmid is the most commonly used form of expression vector. However, the description is intended to include such other forms of expression vectors that serve equivalent functions and which are, or become, known in the art.

The term “operably linked” refers to juxtaposition wherein the elements are in an arrangement allowing them to be functionally related. For example, a promoter is operably linked to a coding sequence if it controls the transcription of the coding sequence.

Tissues

In one embodiment, the tissue or organ is the alimentary canal or a section thereof (e.g. the oesophagus, the stomach or the intestine such as the small intestine or the large intestine and colon) or another mucosal sites (such as the nasal passages and the lungs).

In one embodiment, the tissue or organ is the alimentary canal or part thereof.

Examples of parts of the alimentary canal include the oesophagus, the stomach and the intestine (such as the small intestine (e.g. the duodenum, the jejunum and the ileum) and/or the large intestine (e.g. the caecum, ascending colon, transverse colon, descending colon, and sigmoid colon)).

Subject

In one embodiment, the subject is a monogastric animal.

Examples of monogastric animals include poultry, humans, rats, pigs, dogs, cats, horses and rabbits.

In another embodiment, the subject is a mammal such as a monogastric mammal.

Examples of monogastric mammals include omnivores (such as humans, rats, and pigs), carnivores (such as dogs and cats), and herbivores (such as horses and rabbits).

In one embodiment, the subject is a human.

Typically, TLR5 is capable of being expressed in the cells of said subject.

Disorders

Roseburia flagellin, and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), may be used in treating a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder.

In one embodiment, the inflammatory disorder and/or an autoimmune disorder affects the alimentary canal, or a section thereof, of said subject.

In one embodiment, the inflammatory disorder and/or an autoimmune disorder affects a mucosal site of a subject. Examples of mucosal sites include the alimentary canal or a section thereof (e.g. the oesophagus, the stomach or the intestine such as the small intestine or the large intestine and colon), the nasal passages and the lungs.

In one embodiment, the inflammatory disorder and/or an autoimmune disorder is selected from the group consisting of rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, coeliac disease, atopic dermatitis, rhinitis, irritable bowel syndrome (IBS), colitis, inflammatory bowel disorder (IBD), ulcerative colitis, pouchitis, Crohn's disease, functional dyspepsia, atopic diseases, necrotising enterocolitis, and combinations thereof.

In one aspect, the inflammatory disorder is colitis. In a further aspect, the inflammatory disease is Crohn's disease, ulcerative colitis or pouchitis.

In one aspect, the inflammatory disorder and/or an autoimmune disorder affects the intestine.

In one aspect, the intestinal disorder is IBS. The precise pathophysiology of IBS remains to be elucidated. Recent studies have described mucosal inflammation and alterations in intestinal microbiota in IBS patients and a disease correlation with intestinal infections.

In a further aspect, the intestinal disorder is Crohn's disease.

In one aspect, the disorder is an autoimmune disorder.

In one aspect, the autoimmune disorder is selected from the group consisting of ulcerative colitis, pouchitis, rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, allergies (including coeliac disease), atopic dermatitis and rhinitis.

In particular due to its function in restoring immune tolerance, the autoimmune diseases, rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes are of particular relevance.

As used herein, the term “medicament” encompasses medicaments for both human and animal usage in human and veterinary medicine. In addition, the term “medicament” as used herein means any substance, which provides a therapeutic and/or beneficial effect. The term “medicament” as used herein is not necessarily limited to substances, which need Marketing Approval, but may include substances which, can be used in cosmetics, nutraceuticals, food (including feeds and beverages for example), probiotic cultures, nutritional supplements and natural remedies. In addition, the term “medicament” as used herein encompasses a product designed for incorporation in animal feed, for example livestock feed and/or pet food.

Prophylactic Applications

The Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), according to the invention may also be used in prophylactic applications. In prophylactic applications, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), according to the invention are administered to a patient susceptible to, or otherwise at risk of, a particular disease in an amount that is sufficient to at least partially reduce the risk of developing a disease. Such an amount is defined to be “a prophylactic effective dose”. The precise amounts depend on a number of specific factors such as the subject's state of health and weight.

Encapsulation

In one embodiment, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin of the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is encapsulated.

In a further embodiment, the pharmaceutical composition comprising the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is encapsulated.

In another embodiment, the nutritional supplement comprising the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), is encapsulated.

In a further embodiment, the feedstuff, food product, dietary supplement, or food additive is encapsulated.

The term “encapsulated” as used here refers to a means for protecting the polypeptide, and/or polynucleotide sequence, and/or the vector, and/or the host cell, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), from an incompatible environment by physical separation so that it can be delivered to the target site (e.g. the intestine) without degradation or significant degradation in order that the polypeptide, and/or polynucleotide sequence, and/or the vector, and/or the host cell, and/or the Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), can have an effect on the target site. An example is an enteric coated capsule.

Even when the objective of the encapsulation is the isolation of the polypeptide, and/or polynucleotide sequence, and/or the vector, and/or the host cell, and/or the Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), from its surroundings, the protective coating or shell must be ruptured at the time of desired action.

The rupturing of the protective coating or shell is typically brought about through the application of chemical and physical stimuli such as pressure, enzyme attack, chemical reaction and physical disintegration.

For example, the encapsulation ensures that the polypeptide, and/or polynucleotide sequence, and/or the vector, and/or the host cell, and/or the Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), can be ingested so that the polypeptide, and/or polynucleotide sequence, and/or the vector, and/or the host cell and/or the Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), can be delivered to the intestine (i.e. the target site) in an amount which is effective to produce an effect in the intestine.

Pharmaceutical Composition

The pharmaceutical composition may be any pharmaceutical composition. In one aspect, the pharmaceutical composition is to be administered orally, enterally or rectally. For example, the composition may be an edible composition. “Edible” means a material that is approved for human or animal consumption.

The pharmaceutical compositions may be for human or animal usage in human and veterinary medicine.

Examples of such suitable excipients for the various different forms of pharmaceutical compositions described herein may be found in the “Handbook of Pharmaceutical Excipients, 2nd Edition, (1994), Edited by A Wade and P J Weller.

Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985).

Examples of suitable carriers include lactose, starch, glucose, methyl cellulose, magnesium stearate, mannitol, sorbitol and the like. Examples of suitable diluents include ethanol, glycerol and water.

The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. The pharmaceutical compositions may comprise as, or in addition to, the carrier, excipient or diluent any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s).

Examples of suitable binders include starch, gelatin, natural sugars such as glucose, anhydrous lactose, free-flow lactose, beta-lactose, corn sweeteners, natural and synthetic gums, such as acacia, tragacanth or sodium alginate, carboxymethyl cellulose and polyethylene glycol.

Examples of suitable lubricants include sodium oleate, sodium stearate, magnesium stearate, sodium benzoate, sodium acetate, sodium chloride and the like.

Preservatives, stabilizers, dyes and even flavouring agents may be provided in the pharmaceutical composition. Examples of preservatives include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. Antioxidants and suspending agents may be also used.

Nutritional Supplements

Nutritionally acceptable carriers, diluents and excipients include those suitable for human or animal consumption and that are used as standard in the food industry. Typical nutritionally acceptable carriers, diluents and excipients will be familiar to the skilled person in the art.

Feedstuff/Products

A further aspect of the invention relates to feedstuffs, food products, dietary supplements and food additives containing Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis).

The terms “feedstuff”, “food product” “food additive” and “dietary supplement” as used herein are intended to cover all consumable products that can be solid, jellied or liquid.

Suitable food products may include, for example, functional food products, food compositions, pet food, livestock feed, health foods, feedstuffs and the like. In one aspect, the food product is a health food.

As used herein, the term “functional food product” means food that is capable of providing not only a nutritional effect, but is also capable of delivering a further beneficial effect to the consumer. Accordingly, functional foods are ordinary foods that have components or ingredients (such as those described herein) incorporated into them that impart to the food a specific functional—e.g. medical or physiological benefit—other than a purely nutritional effect.

Examples of specific food products that are applicable to the present invention include milk-based products, ready to eat desserts, powders for re-constitution with, e.g., milk or water, chocolate milk drinks, malt drinks, ready-to-eat dishes, instant dishes or drinks for humans or food compositions representing a complete or a partial diet intended for pets or livestock.

In one aspect, the feedstuff, food product, dietary supplement or food additive according to the present invention are intended for humans, pets or livestock such as monogastric animals. The feedstuff, food product, dietary supplement or food additive may be intended for animals selected from the group consisting of dogs, cats, pigs, horses, or poultry. In a further embodiment, the food product, dietary supplement or food additive is intended for adult species, in particular human adults.

The term “milk-based product” as used herein means any liquid or semi-solid milk or whey based product having a varying fat content. The milk-based product can be, e.g., cow's milk, goat's milk, sheep's milk, skimmed milk, whole milk, milk recombined from powdered milk and whey without any processing, or a processed product, such as yoghurt, curdled milk, curd, sour milk, sour whole milk, butter milk and other sour milk products. Another important group includes milk beverages, such as whey beverages, fermented milks, condensed milks, infant or baby milks; flavoured milks, ice cream; milk-containing food such as sweets.

The feedstuffs, food products, dietary supplements or food additives of the present invention may be—or may be added to—food supplements, also referred to herein as dietary or nutritional supplements or food additives.

The feedstuffs, food products, dietary supplements or food additives according to the invention may also be used in animal nutrition (e.g. in pig nutrition), particularly in the early-weaned period and growing fattening period. The feedstuffs, food products, dietary supplements or food additives are expected to enhance immune function reduce and prevent infectious diseases, beneficially alter the microbiota composition, and improve growth and performance of animals, for example, through increased feed conversion efficiency.

Probiotics or Live Biotherapeutic Product

The Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), may be used in a probiotic or live biotherapeutic product.

Another aspect of the invention relates to a probiotic composition comprising the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or said polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis).

As used herein, the term “probiotic” means microbial cell preparations or components of microbial cells with a beneficial effect on the health or well-being of the host. (Salminen S, Ouwehand A. Benno Y. et al “Probiotics: how should they be defined” Trends Food Sci. Technol. 1999:10 107-10).

In one aspect, the probiotic composition is an orally administrable composition of metabolically active, i.e., live and/or or lyophilized, or non-viable heat-killed, irradiated or lysed probiotic bacteria. The probiotic composition may contain other ingredients. The probiotic composition can be administered orally, i.e., in the form of a tablet, capsule or powder. The probiotic composition may comprise the bacterial species R. hominis or R. intestinalis. Encapsulated products are favoured for R. hominis and R. intestinalis as they are anaerobes. Other ingredients (such as vitamin C, for example), may be included as oxygen scavengers and prebiotic substrates (such as these improve the colonisation and survival in vivo). Alternatively, the probiotic composition of the invention may be administered orally as a food or nutritional product, such as milk or whey based fermented dairy product, or as a pharmaceutical product.

A suitable daily dose of the probiotic bacteria is from about 1×10³ to about 1×10¹¹ colony forming units (CFU); for example, from about 1×10⁷ to about 1×10¹⁰ CFU; in another example from about 1×10⁶ to about 1×10¹⁰ CFU.

In one aspect, the probiotic composition contains the bacterial species and/or cellular components thereof, as active ingredients, in an amount of from about 1×10⁶ to about 1×10¹¹ CFU/g, respect to the weight of the composition; for example, from about 1×10⁸ to about 1×10¹⁰ CFU/g. The dose may be of 1 g, 3 g, 5 g, and 10 g.

Typically, a probiotic is optionally combined with at least one suitable prebiotic compound. A prebiotic is usually a non-digestible carbohydrate such as an oligo- or polysaccharide, or a sugar alcohol, which is not degraded or absorbed in the upper digestive tract. Known prebiotics include commercial products such as inulin and transgalacto-oligosaccharides.

In one aspect, the probiotic composition of the present invention includes a prebiotic in an amount of from about 1 to about 30% by weight, respect to the total weight composition, (e.g. from 5 to 20% by weight). Carbohydrates may be selected from the group consisting of: fructo-oligosaccharides (or FOS), short-chain fructo-oligosaccharides, inulin, isomalt-oligosaccharides, pectins, xylo-oligosaccharides (or XOS), chitosan-oligosaccharides (or COS), beta-glucans, arable gum modified and resistant starches, polydextrose, D-tagatose, acacia fibers, carob, oats, and citrus fibers. In one aspect, the prebiotics are the short-chain fructo-oligosaccharides (for simplicity shown herein below as FOSs-c.c); said FOSs-c.c. are not digestible carbohydrates, generally obtained by the conversion of the beet sugar and including a saccharose molecule to which three glucose molecules are bonded.

Administration

The pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention may be adapted for oral, rectal, vaginal, parenteral, intramuscular, intraperitoneal, intraarterial, intrathecal, intrabronchial, subcutaneous, intradermal, intravenous, nasal, buccal or sublingual routes of administration.

In one aspect, the pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention are adapted for oral, rectal, vaginal, parenteral, nasal, buccal or sublingual routes of administration.

In a further aspect, the pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives of the present invention are adapted for oral administration.

For oral administration, particular use is made of compressed tablets, pills, tablets, gellules, drops, and capsules.

Other forms of administration comprise solutions or emulsions which may be injected intravenously, intraarterially, intrathecally, subcutaneously, intradermally, intraperitoneally or intramuscularly, and which are prepared from sterile or sterilisable solutions. The pharmaceutical compositions of the present invention may also be in form of suppositories, pessaries, suspensions, emulsions, lotions, ointments, creams, gels, sprays, solutions or dusting powders.

An alternative means of transdermal administration is by use of a skin patch. For example, the active ingredient can be incorporated into a cream consisting of an aqueous emulsion of polyethylene glycols or liquid paraffin. In another example, the active ingredient can also be incorporated into an ointment consisting of a white wax or white soft paraffin base together with such stabilisers and preservatives as may be required.

Pharmaceutical compositions, the nutritional supplements, feedstuffs, food products, dietary supplements or food additives may be formulated in unit dosage form, i.e., in the form of discrete portions containing a unit dose, or a multiple or sub-unit of a unit dose.

Dosage

A person of ordinary skill in the art can easily determine an appropriate dose of the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), to administer to a subject without undue experimentation. Typically, a physician will determine the actual dosage which will be most suitable for an individual patient and it will depend on a variety of factors including the activity of the specific bacterial strain employed, the metabolic stability and length of action of that strain, the age, body weight, general health, sex, diet, mode and time of administration, rate of excretion, drug combination, the severity of the particular condition, and the individual undergoing therapy. The dosages disclosed herein are exemplary of the average case. There can of course be individual instances where higher or lower dosage ranges are merited, and such are within the scope of this invention.

Combinations

In one aspect, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), are administered in combination with at least one or two, or three or four or five other active agents. In such cases, the Roseburia flagellin, and/or the polypeptide Fla (such as FlaA1 or FlaA2), and/or a polynucleotide sequence encoding said Roseburia flagellin and/or polypeptide Fla (such as FlaA1 or FlaA2), and/or the vector comprising said polynucleotide sequence, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, and/or Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), may be administered consecutively, simultaneously or sequentially with the one or more other active agents.

The at least one or two, or three or four or five other active agents may be selected from the group consisting of: Roseburia flagellins, the polypeptide Fla (such as FlaA1 or FlaA2), polynucleotide sequence(s) encoding said Roseburia flagellin, polynucleotide sequence(s) encoding said polypeptide Fla (such as FlaA1 or FlaA2), vector(s) comprising said polynucleotide sequence(s), host cell(s) comprising said vector(s), host cell(s) comprising said polynucleotide sequence(s), and microorganisms (e.g. Roseburia such as R. hominis and/or R. intestinalis).

The at least one or two, or three or four or five other active agents may be a microorganism (e.g. a Roseburia such as R. hominis and/or R. intestinalis). Examples of suitable microorganisms include: Roseburia hominis A2-183 and Roseburia intestinalis L1-82.

Sequence Identity or Sequence Homology

The terms “polypeptide”, “polypeptide sequence”, “protein” and “amino acid sequence” are used interchangeably herein.

The terms “polynucleotide sequence” and “nucleotide sequence” are used interchangeably herein.

The present invention also encompasses the use of sequences having a degree of sequence identity or sequence homology with amino acid sequence(s) of a polypeptide described herein (e.g. variants, homologues and derivatives) or of any nucleotide sequence encoding such a polypeptide (hereinafter referred to as a “homologous sequence(s)”). Here, the term “homologue” means an entity having a certain homology with the subject amino acid sequences and the subject nucleotide sequences. Here, the term “homology” can be equated with “identity”.

In the present context, a homologous sequence is taken to include an amino acid or a nucleotide sequence which may be at least 50, 60, 70, 75, 80, 85 or 90% identical, in some embodiments at least 95, 96, 97, 98 or 99% identical to the subject sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity.

In some embodiments, a homologous sequence is taken to include an amino acid sequence or nucleotide sequence which has one or several additions, deletions and/or substitutions compared with the subject sequence.

In some embodiments, the present invention relates to the use of a protein whose amino acid sequence is represented herein or a protein derived from this (parent) protein by substitution, deletion or addition of one or several amino acids, such as 2, 3, 4, 5, 6, 7, 8, 9 amino acids, or more amino acids, such as 10 or more than 10 amino acids in the amino acid sequence of the parent protein and having the activity of the parent protein.

In some embodiments, the present invention relates to the use of a nucleic acid sequence (or gene) encoding a protein whose amino acid sequence is represented herein or encoding a protein derived from this (parent) protein by substitution, deletion or addition of one or several amino acids, such as 2, 3, 4, 5, 6, 7, 8, 9 amino acids, or more amino acids, such as 10 or more than 10 amino acids in the amino acid sequence of the parent protein and having the activity of the parent protein.

In the present context, a homologous sequence is taken to include a nucleotide sequence which may be at least 50, 60, 70, 75, 85 or 90% identical, in some embodiments at least 95, 96, 97, 98 or 99% identical to a nucleotide sequence encoding a polypeptide described herein (the subject sequence). Typically, the homologues will comprise the same or equivalent sequences that code for the domain(s) etc. as the subject sequence. Although homology can also be considered in terms of similarity (i.e. amino acid residues having similar chemical properties/functions), in the context of the present invention it is preferred to express homology in terms of sequence identity.

The homologous amino acid sequence and/or nucleotide sequence may provide and/or encode a polypeptide which retains the functional activity and/or enhances the activity of the polypeptide.

In some aspects, an amino acid sequence as described herein has at least 50, 60, 70, 75, 80, 85 or 90% identity, in some embodiments at least 95, 96, 97, 98 or 99% identity to the subject sequence.

In some aspects, a nucleotide sequence as described herein has at least 50, 60, 70, 75, 80, 85 or 90% identity, in some embodiments at least 95, 96, 97, 98 or 99% identity to the subject sequence.

Homology comparisons can be conducted by eye, or more usually, with the aid of readily available sequence comparison programs. These commercially available computer programs can calculate % homology between two or more sequences.

% homology may be calculated over contiguous sequences, i.e. one sequence is aligned with the other sequence and each amino acid in one sequence is directly compared with the corresponding amino acid in the other sequence, one residue at a time. This is called an “ungapped” alignment. Typically, such ungapped alignments are performed only over a relatively short number of residues.

Although this is a very simple and consistent method, it fails to take into consideration that, for example, in an otherwise identical pair of sequences, one insertion or deletion will cause the following amino acid residues to be put out of alignment, thus potentially resulting in a large reduction in % homology when a global alignment is performed. Consequently, most sequence comparison methods are designed to produce optimal alignments that take into consideration possible insertions and deletions without penalizing unduly the overall homology score. This is achieved by inserting “gaps” in the sequence alignment to try to maximize local homology.

However, these more complex methods assign “gap penalties” to each gap that occurs in the alignment so that, for the same number of identical amino acids, a sequence alignment with as few gaps as possible—reflecting higher relatedness between the two compared sequences—will achieve a higher score than one with many gaps. “Affine gap costs” are typically used that charge a relatively high cost for the existence of a gap and a smaller penalty for each subsequent residue in the gap. This is the most commonly used gap scoring system. High gap penalties will of course produce optimized alignments with fewer gaps. Most alignment programs allow the gap penalties to be modified. Typically the default values are used when using such software for sequence comparisons.

Calculation of maximum % homology therefore firstly requires the production of an optimal alignment, taking into consideration gap penalties. A suitable computer program for carrying out such an alignment is the Vector NTI (Invitrogen Corp.). Examples of software that can perform sequence comparisons include, but are not limited to, the BLAST package (see Ausubel et al 1999 Short Protocols in Molecular Biology, 4th Ed—Chapter 18), BLAST 2 (see FEMS Microbiol Lett 1999 174(2): 247-50; FEMS Microbiol Lett 1999 177(1): 187-8 and, FASTA (Altschul et al 1990 J. Mol. Biol. 403-410) and AlignX for example. At least BLAST, BLAST 2 and FASTA are available for offline and online searching (see Ausubel et al 1999, pages 7-58 to 7-60).

Although the final % homology can be measured in terms of identity, the alignment process itself is typically not based on an all-or-nothing pair comparison. Instead, a scaled similarity score matrix is generally used that assigns scores to each pairwise comparison based on chemical similarity or evolutionary distance. An example of such a matrix commonly used is the BLOSUM62 matrix—the default matrix for the BLAST suite of programs. Vector NTI programs generally use either the public default values or a custom symbol comparison table if supplied (see user manual for further details). For some applications, it is preferred to use the default values for the Vector NTI package.

Alternatively, percentage homologies may be calculated using the multiple alignment feature in Vector NTI (Invitrogen Corp.), based on an algorithm, analogous to CLUSTAL (Higgins D G & Sharp P M (1988), Gene 73(1), 237-244).

Once the software has produced an optimal alignment, it is possible to calculate % homology, for example % sequence identity. The software typically does this as part of the sequence comparison and generates a numerical result.

Should Gap Penalties be used when determining sequence identity, then the following parameters can be used for pairwise alignment for example:

TABLE-US-00017 FOR BLAST GAP OPEN 0 GAP EXTENSION 0 FOR CLUSTAL DNA PROTEIN WORD SIZE 2 1 K triple GAP PENALTY 15 10 GAP EXTENSION 6.66 0.1

In one embodiment, CLUSTAL may be used with the gap penalty and gap extension set as defined above.

In one embodiment, the degree of identity with regard to a nucleotide sequence is determined over at least 20 contiguous nucleotides, for example over at least 30 contiguous nucleotides, for example over at least 40 contiguous nucleotides, for example over at least 50 contiguous nucleotides, for example over at least 60 contiguous nucleotides, for example over at least 100 contiguous nucleotides, for example over at least 200 contiguous nucleotides, for example over at least 300 contiguous nucleotides.

In one embodiment, the degree of identity with regard to a nucleotide sequence may be determined over the whole sequence.

Recombinant

In one aspect the Roseburia flagellin polypeptide and/or polynucleotide sequence for use in the present invention is a recombinant sequence—i.e. a sequence that has been prepared using recombinant DNA techniques.

These recombinant DNA techniques are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Cold Spring Harbor Laboratory Press.

Synthetic

In one aspect the Roseburia flagellin polynucleotide sequence for use in the present invention is a synthetic sequence—i.e. a sequence that has been prepared by in vitro chemical or enzymatic synthesis. It includes, but is not limited to, sequences made with optimal codon usage for host organisms—such as the methylotrophic yeasts Pichia and Hansenula.

(A) Expression of Enzymes

The nucleotide sequence for use in the present invention may be incorporated into a recombinant replicable vector. The vector may be used to replicate and express the nucleotide sequence, in protein form, in and/or from a compatible host cell.

Expression may be controlled using control sequences e.g. regulatory sequences.

The protein produced by a host recombinant cell by expression of the nucleotide sequence may be secreted or may be contained intracellularly depending on the sequence and/or the vector used. The coding sequences may be designed with signal sequences which direct secretion of the substance coding sequences through a particular prokaryotic or eukaryotic cell membrane.

(B) Expression Vector

In one aspect, the present invention relates to a vector (such as an expression vector) comprising at least one polynucleotide sequence encoding at least one Roseburia flagellin.

The term “expression vector” means a construct capable of in vivo or in vitro expression.

In one embodiment, the expression vector is incorporated into the genome of a suitable host organism. The term “incorporated” in one aspect covers stable incorporation into the genome.

The nucleotide sequence of the present description may be present in a vector in which the nucleotide sequence is operably linked to regulatory sequences capable of providing for the expression of the nucleotide sequence by a suitable host cell or host organism.

The vectors for use in the present invention may be transformed into a suitable host cell or host organism as described herein to provide for expression of a polypeptide of the present description.

The choice of vector e.g. a plasmid, cosmid, or phage vector will often depend on the host cell into which it is to be introduced.

The vectors for use in the present invention may contain one or more selectable marker genes-such as a gene, which confers antibiotic resistance e.g. ampicillin, kanamycin, chloramphenicol or tetracyclin resistance. Alternatively, the selection may be accomplished by co-transformation (as described in WO91/17243).

Vectors may be used in vitro, for example for the production of RNA or used to transfect, transform, transduce or infect a host cell.

Thus, in a further embodiment, the description provides a method of making nucleotide sequences of the present description by introducing a nucleotide sequence of the present description into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector.

The vector may further comprise a nucleotide sequence enabling the vector to replicate in the host cell in question. Examples of such sequences are the origins of replication of plasmids pUC19, pACYC177, pUB110, pE194, pAMB1 and pIJ702.

An expression vector may comprise at least two, three, four or five polynucleotide sequences encoding Roseburia flagellins.

Examples of expression vectors include pGEX-6P-1, pCR-Blunt II-TOPO and T7-MAT-Tag-FLAG-.

The expression vector pGEX-6P-1 may be used for cloning recombinant flagellins. The expression vector pGEX-6P-1 comprises a tac promoter for chemically inducible, high-level expression of GST-tagged recombinant proteins, an internal lacIq gene for use in any E. coli host, an AmpR gene for ampicillin selection and a PreScission Protease site for cleaving, if desired, the protein from the fusion product.

The cloning vector pCR-Blunt II-TOPO may be used for cloning recombinant flagellins, in particular those which are insoluble after cell lysis. Typically this vector allows high-efficiency DNA cloning of blunt-end PCR products. The vector comprises Kanamycin and Zeocin resistance genes for selection in E. coli, and the insert is flanked by multiples restriction sites for excision.

Expression vector T7-MAT-Tag-FLAG- may be used for cloning recombinant flagellins, in particular those which insoluble after cell lysis. The multi cloning site (MCS) is flanked by MAT (Metal Affinity Tag) sequence and FLAG peptide (Asp-Tyr-Lys-Asp-Asp-Asp-Asp-Lys; SEQ ID NO: 13) sequence, which results in the production of double-tagged flagellin, which can be further purified by affinity columns. This expression vector also comprises a pT7/lac (phage T7 lac operon) promoter for IPTG inducible, high-level expression of MAT-ORF-FLAG recombinant flagellins, an internal lad gene that represses transcription at basal state in any E. coli host, and an AmpR gene for ampicillin selection.

(C)

(D) Regulatory Sequences

In some applications, the nucleotide sequence for use in the present invention is operably linked to a regulatory sequence which is capable of providing for the expression of the nucleotide sequence, such as by the chosen host cell. By way of example, the present invention covers a vector comprising the nucleotide sequence of the present invention operably linked to such a regulatory sequence, i.e. the vector is an expression vector.

The term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A regulatory sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under condition compatible with the control sequences.

The term “regulatory sequences” includes promoters and enhancers and other expression regulation signals.

The term “promoter” is used in the normal sense of the art, e.g. an RNA polymerase binding site.

Enhanced expression of the nucleotide sequence encoding a flagellin of the present description may also be achieved by the selection of heterologous regulatory regions, e.g. promoter, secretion leader and terminator regions.

In one embodiment, the nucleotide sequence according to the present description is operably linked to at least a promoter.

Other promoters may even be used to direct expression of the polypeptide of the present description.

Examples of suitable promoters for directing the transcription of the nucleotide sequence in a bacterial, fungal or yeast host are well known in the art.

The promoter can additionally include features to ensure or to increase expression in a suitable host. For example, the features can be conserved regions such as a Pribnow Box or a TATA box.

(E) Constructs

The term “construct”—which is synonymous with terms such as “conjugate”, “cassette” and “hybrid”—includes a nucleotide sequence for use according to the present invention directly or indirectly attached to a promoter.

An example of an indirect attachment is the provision of a suitable spacer group such as an intron sequence, such as the Sh1-intron or the ADH intron, intermediate the promoter and the nucleotide sequence of the present description. The same is true for the term “fused” in relation to the present description which includes direct or indirect attachment. In some cases, the terms do not cover the natural combination of the nucleotide sequence coding for the protein ordinarily associated with the wild type gene promoter and when they are both in their natural environment.

The construct may even contain or express a marker, which allows for the selection of the genetic construct.

For some applications, the construct of the present description comprises at least the nucleotide sequence of the present description operably linked to a promoter.

(F)

(G) Host Cells

The term “host cell”—in relation to the present description includes any cell that comprises the nucleotide sequence and/or an expression vector as described herein. Typically the host cell is capable of the recombinant production of a protein having the specific properties as defined herein.

Examples of host cells include bacteria such as Roseburia spp. and competent cells. Examples of Roseburia spp are Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, and Roseburia inuhnivorans. Examples of competent cells include competent E. coli cells (such as E. coli BL21(DE3) pLysS and/or E. coli B21 Rosetta).

Thus, a further embodiment of the present description provides host cells transformed or transfected with a nucleotide sequence of the present description. In addition, or alternatively, a further embodiment of the present description provides host cells transformed or transfected with a nucleotide sequence (e.g. a promoter such as a heterologous promoter or an exogenous) that is capable of upregulating (overexpressing) the expression of a nucleotide sequence (e.g. gene—such as a homologous gene or an endogenous gene) encoding a flagellin of the present description when compared to the equivalent microorganism prior to transformation. The cells will be chosen to be compatible with the said vector and may for example be bacterial (e.g. prokaryotic), fungal, or yeast cells.

The nucleotide sequence encoding the flagellin of the present description may be heterologous or homologous to the host cell. Typically when the nucleotide sequence encoding the flagellin is homologous to the host cell the host cell comprises multiple copies of the nucleotide sequence. In addition or alternatively, the nucleotide sequence encoding the flagellin is operably linked to a heterologous promoter; typically said promoter is capable of upregulating (overexpressing) the homologous nucleotide sequence encoding the flagellin.

In one example, the host cell comprises the nucleotide sequence coding for the flagellin polypeptide of the present description (such as a homologous or endogenous nucleotide sequence) under the control of a heterologous or exogenous promoter.

In one embodiment, the host cell is transformed or transfected with one or more nucleotide sequences that encodes at least one flagellin (e.g. Roseburia flagellin) selected from the group consisting of Fla1, Fla2, Fla3 and Fla4. In another embodiment, the host cell is transformed or transfected with one or more nucleotide sequences that encode at least one flagellin (e.g. Roseburia flagellin) selected from the group consisting of Fla2, Fla1 and Fla4. In a further embodiment, the host cell is transformed or transfected with a nucleotide sequences that encodes the flagellin (e.g. Roseburia flagellin) Fla2.

The host cell may comprise multiple copies of polynucleotide sequences encoding Roseburia flagellins.

A host cell may comprise at least 1, 2, 3, 4 or 5 polynucleotide sequences encoding at least 1, 2, 3, 4 or 5 Roseburia flagellins.

In one embodiment, the host cell comprises a polynucleotide sequence encoding at least one Roseburia flagellin derived or derivable from one Roseburia species and at least one further polynucleotide sequence encoding at least one Roseburia flagellin derived or derivable from a different Roseburia species. For example, the host cell comprises at least one polynucleotide sequence encoding an R. hominis flagellin (e.g. Fla1 or Fla2) and at least one polynucleotide sequence encoding a R. intestinalis flagellin (e.g. Fla1 or Fla 2).

A host cell may comprise at least 1, 2, 3, 4 or 5 expression vectors comprising at least 1, 2, 3, 4 or 5 polynucleotide sequences encoding Roseburia flagellin.

In one embodiment, the host cell comprises an expression vector comprising a polynucleotide sequence encoding Roseburia flagellins derived or derivable from one Roseburia species and at least one further expression vector comprising a polynucleotide sequence encoding Roseburia flagellins derived or derivable from a different Roseburia species. For example, the host cell comprises at least one expression vector comprising a polynucleotide sequence encoding an R. hominis flagellin (e.g. Fla1 or Fla2) and at least one expression vector comprising a polynucleotide sequence encoding a R. intestinalis flagellin (e.g. Fla1 or Fla 2).

The nucleotide sequence encoding the flagellin may be endogenous or exogenous to the host cell. Typically when the nucleotide sequence encoding the flagellin is endogenous to the host cell the host cell comprises multiple copies of the nucleotide sequence. In addition or alternatively, the nucleotide sequence encoding the flagellin is operably linked to an exogenous promoter; typically said promoter is capable of upregulating (overexpressing) the endogenous nucleotide sequence encoding the flagellin.

Examples of suitable bacterial host organisms are gram positive or gram negative bacterial species.

In one embodiment, the host cell is a microorganism.

In one embodiment, the host cell is a lactic acid bacterium species, Lactococcus species, a Bifidobacterium species, a Lactobacillus species or a Propionibacterium species. Examples of lactic acid bacteria include, but are not limited to, Lactobacillus spp., Leuconostoc spp., Pediococcus spp., Lactococcus spp., Streptococcus spp., Aerococcus spp., Carnobacterium spp., Enterococcus spp., Oenococcus spp., Sporolactobacillus spp., Tetragenococcus spp., Vagococcus spp., and Weisella spp.

Examples of Lactobacillus spp include Lactobacillus paracasei, L. acidophilus, L. fermentum, L. brevis, L. gasseri, L. plantarum, L. bulgaricus, L. helveticus, L. reuteri, L. casei, L. jensenii, L. rhamnosus, L. crispatus, L. johnsonii, L. salivarius, L. acetotolerans, L. acidifarinae, L. acidipiscis, L. agilis, L. algidus, L. alimentarius, L. amylolyticus, L. amylophilus, L. amylotrophicus, L. amylovorus, L. animalis, L. antri, L. apodemi, L. aviarius, L. bifermentans, L. buchneri, L. camelliae, L. catenaformis, L. ceti, L. coleohominis, L. collinoides, L. composti, L. concavus, L. coryniformis, L. crustorum, L. curvatus, L. delbrueckii subsp. delbrueckii, L. delbrueckii subsp. bulgaricus, L. delbrueckii subsp. lactis, L. dextrinicus, L. diolivorans, L. equi, L. equigenerosi, L. farraginis, L. farciminis, L. fornicalis, L. fructivorans, L. frumenti, L. fuchuensis, L. galUnarum, L. gastricus, L. ghanensis, L. graminis, L. hammesii, L. hamsteri, L. harbinensis, L. hayakitensis, L. hilgardii, L. homohiochii, L. finers, L. ingluviei, L. intestinalis, L. kalixensis, L. kefiranofaciens, L. kefiri, L. kimchii, L. kitasatonis, L. kunkeei, L. leichmannii, L. lindneri, L. malefermentans, L. mail, L. manihotivorans, L. mindensis, L. mucosae, L. murinus, L. nagelii, L. namurensis, L. nantensis, L. oligofermentans, L. oris, L. panis, L. pantheris, L. parabrevis, L. parabuchneri, L. paracollinoides, L. parafarraginis, L. parakefiri, L. paralimentarius, L. paraplantarum, L. pentosus, L. perolens, L. pontis, L. psittaci, L. rennini, L. rimae, L. rogosae, L. rossiae, L. ruminis, L. saerimneri, L. sakei, L. sanfranciscensis, L. satsumensis, L. secaliphilus, L. sharpeae, L. siliginis, L. spicheri, L. suebicus, L. thailandensis, L. ultunensis, L. vaccinostercus, L. vaginalis, L. versmoldensis, L. vini, L. vitulinus, L. zeae, and L. zymae.

Examples of Propionibacterium include, but are not limited to Propionibacterium freudenrechli subsp. shermanii (PAB), Propionibacterium acidifaciens, Propionibacterium acidipropionici, Propionibacterium acnes, Propionibacterium australiense, Propionibacterium avidum, Propionibacterium cyclohexanicum, Propionibacterium freudenrelchli subsp. freudenrelchli, Propionibacterium granulosum, Propionibacterium jensenii, Propionibacterium microaerophilum, Propionibacterium propionicum, and Propionibacterium thoenii.

In one embodiment, the Propionibacterium is Propionibacterium freudenrechli subsp. shermanii (PAB).

Examples of Bifidobacterium include, but are not limited to, Bifidobacterium adolescentis, B. breve, B. longum, B. animalis, B. infantis, B. thermophilum, B. bifidum, Bifidobacterium catenulatum, Bifidobacterium pseudocatenulatum, Bifidobacterium angulatum and B. lactis.

In another embodiment, the host cell is a Firmicute—for example a Roseburia species such as Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, or Roseburia inulinivorans). In one embodiment, the host cell comprises at least one heterologous polynucleotide sequence encoding a Roseburia flagellin. In addition or alternatively, the host cell comprises at least two copies of a homologous polynucleotide sequence encoding a Roseburia flagellin; for instance, the host cell comprises at least 3, 4 or 5 homologous copies of a polynucleotide sequence encoding a Roseburia flagellin.

Depending on the nature of the nucleotide sequence encoding the polypeptide of the present description, and/or the desirability for further processing of the expressed protein, eukaryotic hosts such as yeasts or other fungi may be used. In general, yeast cells are used over fungal cells because they are easier to manipulate. However, some proteins are either poorly secreted from the yeast cell, or in some cases are not processed properly (e.g. hyperglycosylation in yeast). In these instances, a different fungal host organism should be selected.

The use of suitable host cells—such as yeast, fungal and plant host cells—may provide for post-translational modifications (e.g. myristoylation, glycosylation, truncation, lipidation and tyrosine, serine or threonine phosphorylation) as may be needed to confer optimal biological activity on recombinant expression products of the present description.

The host cell may be a protease deficient or protease minus strain. This may for example be the protease deficient strain Aspergillus oryzae JaL 125 having the alkaline protease gene named “alp” deleted. This strain is described in WO97/35956.

The term “host cell” does not cover native nucleotide coding sequences in their natural environment when they are under the control of their native promoter which is also in its natural environment.

Organism

The term “organism” in relation to the present description includes any organism that could comprise the nucleotide sequence coding for the polypeptide according to the present description and/or products obtained therefrom, and/or wherein a promoter can allow expression of the nucleotide sequence according to the present description when present in the organism.

Suitable organisms may include a bacterium (such as a prokaryote), a fungus, a yeast or a plant.

The term “transgenic organism” in relation to the present description includes any organism that comprises the nucleotide sequence coding for the polypeptide according to the present description and/or the products obtained therefrom, and/or wherein a promoter can allow expression of the nucleotide sequence according to the present description within the organism. In one embodiment the nucleotide sequence is incorporated in the genome of the organism.

The term “transgenic organism” does not cover native nucleotide coding sequences in their natural environment when they are under the control of their native promoter which is also in its natural environment.

Therefore, the transgenic organism of the present description includes an organism comprising any one of, or combinations of, the nucleotide sequence coding for the polypeptide according to the present description, constructs according to the present description, vectors according to the present description, plasmids according to the present description, cells according to the present description, or the products thereof.

For example the transgenic organism may comprise the nucleotide sequence coding for the polypeptide of the present description (such as a homologous nucleotide sequence) under the control of a heterologous promoter.

Transformation of Host Cells/Organism

As indicated earlier, the host organism can be a prokaryotic or a eukaryotic organism. Examples of suitable prokaryotic hosts include Roseburia hominis, Roseburia cecicola, Roseburia faecis, Roseburia intestinalis, Roseburia inulinivorans, E. coli and Bacillus subtilis.

Teachings on the transformation of prokaryotic hosts is well documented in the art, for example see Sambrook et al (Molecular Cloning: A Laboratory Manual, 2nd edition, 1989, Cold Spring Harbor Laboratory Press). If a prokaryotic host is used then the nucleotide sequence may need to be suitably modified before transformation—such as by removal of introns.

Filamentous fungi cells may be transformed using various methods known in the art—such as a process involving protoplast formation and transformation of the protoplasts followed by regeneration of the cell wall in a manner known. The use of Aspergillus as a host microorganism is described in EP 0 238 023.

Another host organism can be a plant. A review of the general techniques used for transforming plants may be found in articles by Potrykus (Annu Rev Plant Physiol Plant Mol Biol [1991] 42:205-225) and Christou (Agro-Food-Industry Hi-Tech March/April 1994 17-27). Further teachings on plant transformation may be found in EP-A-0449375.

General teachings on the transformation of fungi, yeasts and plants are presented in following sections.

(H) Transformed Fungus

A host organism may be a fungus—such as a mould. Examples of suitable such hosts include any member belonging to the genera Thermomyces, Acremonium, Aspergillus, Penicillium, Mucor, Neurospora, Trichoderma and the like.

In one embodiment, the host organism may be a filamentous fungus.

Transforming filamentous fungi is discussed in U.S. Pat. No. 5,741,665 which states that standard techniques for transformation of filamentous fungi and culturing the fungi are well known in the art. An extensive review of techniques as applied to N. crassa is found, for example in Davis and de Serres, Methods Enzymol (1971) 17A: 79-143.

Further teachings which may also be utilised in transforming filamentous fungi are reviewed in U.S. Pat. No. 5,674,707.

In addition, gene expression in filamentous fungi is taught in in Punt et al. (2002) Trends Biotechnol 2002 May; 20(5):200-6, Archer & Peberdy Crit Rev Biotechnol (1997) 17(4):273-306.

The present description encompasses the production of transgenic filamentous fungi according to the present description prepared by use of these standard techniques.

In one aspect, the host organism can be of the genus Aspergillus, such as Aspergillus niger.

A transgenic Aspergillus according to the present description can also be prepared by following, for example, the teachings of Turner G. 1994 (Vectors for genetic manipulation. In: Martinelli S. D., Kinghorn J. R. (Editors) Aspergillus: 50 years on. Progress in industrial microbiology vol 29. Elsevier Amsterdam 1994. pp. 641-666).

(I) Transformed Yeast

In another embodiment, the transgenic organism can be a yeast.

A review of the principles of heterologous gene expression in yeast are provided in, for example, Methods Mot Blot (1995), 49:341-54, and Curr Opin Biotechnol (1997) October; 8(5):554-60

In this regard, yeast—such as the species Saccharomyces cerevisi or Pichia pastoris (see FEMS Microbiol Rev (2000 24(1):45-66), may be used as a vehicle for heterologous gene expression.

A review of the principles of heterologous gene expression in Saccharomyces cerevisiae and secretion of gene products is given by E Hinchcliffe E Kenny (1993, “Yeast as a vehicle for the expression of heterologous genes”, Yeasts, Vol 5, Anthony H Rose and J Stuart Harrison, eds, 2nd edition, Academic Press Ltd.).

For the transformation of yeast, several transformation protocols have been developed. For example, a transgenic Saccharomyces according to the present description can be prepared by following the teachings of Hinnen et al., (1978, Proceedings of the National Academy of Sciences of the USA 75, 1929); Beggs, J D (1978, Nature, London, 275, 104); and Ito, H et al (1983, J Bacteriology 153, 163-168).

The transformed yeast cells may be selected using various selective markers—such as auxotrophic markers dominant antibiotic resistance markers.

(J)

(K) Transformed Plants/Plant Cells

A host organism suitable for the present description may be a plant. In this respect, the basic principle in the construction of genetically modified plants is to insert genetic information in the plant genome so as to obtain a stable maintenance of the inserted genetic material. A review of the general techniques may be found in articles by Potrykus (Annu Rev Plant Physiol Plant Mol Biol [1991] 42:205-225) and Christou (Agro-Food-Industry Hi-Tech March/April 1994 17-27).

Direct infection of plant tissues by Agrobacterium is a simple technique which has been widely employed and which is described in Butcher D. N. et al., (1980), Tissue Culture Methods for Plant Pathologists, eds.: D. S. Ingrams and J. P. Helgeson, 203-208.

Other techniques for transforming plants include ballistic transformation, the silicon whisker carbide technique (see Frame B R, Drayton P R, Bagnaall S V, Lewnau C J, Bullock W P, Wilson H M, Dunwell J M, Thompson J A & Wang K (1994) Production of fertile transgenic maize plants by silicon carbide whisker-mediated transformation, The Plant Journal 6: 941-948) and viral transformation techniques (e.g. see Meyer P, Heidmann I & Niedenhof I (1992) The use of cassava mosaic virus as a vector system for plants, Gene 110: 213-217).

Further teachings on plant transformation may be found in EP-A-0449375.

Plant cells may be grown and maintained in accordance with well-known tissue culturing methods such as by culturing the cells in a suitable culture medium supplied with the necessary growth factors such as amino acids, plant hormones, vitamins, etc.

In a further aspect, the present description relates to a vector system which carries a nucleotide sequence or construct according to the present description and which is capable of introducing the nucleotide sequence or construct into the genome of an organism, such as a plant. The vector system may comprise one vector, but it may comprise two vectors. In the case of two vectors, the vector system is normally referred to as a binary vector system. Binary vector systems are described in further detail in Gynheung An et al., (1980), Binary Vectors, Plant Molecular Biology Manual A3, 1-19.

One extensively employed system for transformation of plant cells uses the Ti plasmid from Agrobacterium tumefaciens or a Ri plasmid from Agrobacterium rhizogenes An et al., (1986), Plant Physiol. 81, 301-305 and Butcher D. N. et al., (1980), Tissue Culture Methods for Plant Pathologists, eds.: D. S. Ingrams and J. P. Helgeson, 203-208. After each introduction method of the desired promoter or construct or nucleotide sequence according to the present description in the plants, the presence and/or insertion of further DNA sequences may be necessary. If, for example, for the transformation the Ti- or Ri-plasmid of the plant cells is used, at least the right boundary and often however the right and the left boundary of the Ti- and Ri-plasmid T-DNA, as flanking areas of the introduced genes, can be connected. The use of T-DNA for the transformation of plant cells has been intensively studied and is described in EP-A-120516; Hoekema, in: The Binary Plant Vector System Offset-drukkerij Kanters B. B., Alblasserdam, 1985, Chapter V; Fraley, et al., Crit. Rev. Plant Sci., 4:1-46; and An et al., EMBO J. (1985) 4:277-284.

Culturing and Production

Host cells transformed with the nucleotide sequence of the present description and/or an expression vector of the present description may be cultured under conditions conducive to the production of the encoded polypeptide and which facilitate recovery of the polypeptide from the cells and/or culture medium.

The medium used to cultivate the cells may be any conventional medium suitable for growing the host cell in questions and obtaining expression of the polypeptide.

The protein produced by a recombinant cell may be displayed on the surface of the cell.

The protein may be secreted from the host cells and may conveniently be recovered from the culture medium using well-known procedures.

(L) Secretion

In some embodiments, the protein is secreted from the expression host into the culture medium from where the protein may be recovered. According to the present description, the secretion leader sequence may be selected on the basis of the desired expression host. Hybrid signal sequences may also be used with the context of the present description.

Typical examples of heterologous secretion leader sequences are those originating from the fungal amyloglucosidase (AG) gene (glaA—both 18 and 24 amino acid versions e.g. from Aspergillus), the a-factor gene (yeasts e.g. Saccharomyces, Kluyveromyces and Hansenula) or the α-amylase gene (Bacillus).

By way of example, the secretion of heterologous proteins in E. coli is reviewed in Methods Enzymol (1990) 182:132-43.

Detection

A variety of protocols for detecting and measuring the expression of the amino acid sequence are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) and fluorescent activated cell sorting (FACS).

A wide variety of labels and conjugation techniques are known by those skilled in the art and can be used in various nucleic and amino acid assays.

A number of companies such as Pharmacia Biotech (Piscataway, N.J.), Promega (Madison, Wis.), and US Biochemical Corp (Cleveland, Ohio) supply commercial kits and protocols for these procedures.

Suitable reporter molecules or labels include those radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles and the like. Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241.

Also, recombinant immunoglobulins may be produced as shown in U.S. Pat. No. 4,816,567.

(M)

(N) Fusion Proteins

The amino acid sequence for use according to the present description may be produced as a fusion protein, for example to aid in extraction and purification. Examples of fusion protein partners include glutathione-S-transferase (GST), 6×His, GAL4 (DNA binding and/or transcriptional activation domains) and (β-galactosidase). It may also be convenient to include a proteolytic cleavage site between the fusion protein partner and the protein sequence of interest to allow removal of fusion protein sequences.

Typically, the fusion protein will not hinder the activity of the protein sequence.

Gene fusion expression systems in E. coli have been reviewed in Curr Opin Biotechnol (1995) 6(5):501-6.

In another embodiment, the amino acid sequence may be ligated to a heterologous sequence to encode a fusion protein. For example, for screening of peptide libraries for agents capable of affecting the substance activity, it may be useful to encode a chimeric substance expressing a heterologous epitope that is recognised by a commercially available antibody.

The present invention is further described by way of the following non-limiting examples.

Examples

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA and immunology, which are within the capabilities of a person of ordinary skill in the art. Such techniques are explained in the literature. See, for example, J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning: A Laboratory Manual, Second Edition, Books 1-3, Col d Spring Harbor Laboratory Press; Ausubel, F. M. et al. (1995 and periodic supplements; Current Protocols in Molecular Biology, ch. 9, 13, and 16, John Wiley & Sons, New York, N.Y.); B. Roe, J. Crabtree, and A. Kahn, 1996, DNA Isolation and Sequencing: Essential Techniques, John Wiley & Sons; J. M. Polak and James O'D. McGee, 1990, In Situ Hybridization: Principles and Practice; Oxford University Press; M. J. Gait (Editor), 1984, Oligonucleotide Synthesis: A Practical Approach, Irl Press; D. M. J. Lilley and J. E. Dahlberg, 1992, Methods of Enzymology: DNA Structure Part A: Synthesis and Physical Analysis of DNA Methods in Enzymology, Academic Press; and E. M. Shevach and W. Strober, 1992 and periodic supplements, Current Protocols in Immunology, John Wiley & Sons, New York, N.Y. Each of these general texts is herein incorporated by reference.

Material and Methods ROSEBURIA GENUS FLAGELLINS Flagellin Diversity

Flagellins from Roseburia genus bacteria, in particular, Roseburia hominis and Roseburia intestinalis were cloned, expressed, purified and analysed.

FIGS. 18A and 18B show an SDS-Analysis of recombinant flagellins.

Flagellin protein nomenclature:

Roseburia Genus

-   -   Roseburia Species     -   Roseburia hominis         -   Roseburia hominis FlaA1 (This is also referred herein as             RhFlaA1 or Rh1)         -   Roseburia hominis FlaA2 (This is also referred herein as             RhFlaA2 or Rh2)     -   Roseburia intestinalis         -   Roseburia intestinalis FlaA1 (This is also referred herein             as RiFlaA1 or Ri1 or RI1)         -   Roseburia intestinalis FlaA2 (This is also referred herein             as RiFlaA2 or Ri2 or RI2)         -   Roseburia intestinalis FlaA3 (This is also referred herein             as RiFlaA3 or Ri3 or RI3)         -   Roseburia intestinalis FlaA4 (This is also referred herein             as RiFlaA1 or Ri4 or RI4)

See:

-   ELY, B., ELY, T. W., CRYMES, W. B., JR and MINNICH, S. A., 2000. A     family of six flagellin genes contributes to the Caulobacter     crescentus flagellar filament. Journal of Bacteriology, 182(17), pp.     5001-5004. -   IBRAHIM, G. F., FLEET, G. H., LYONS, M. J. and WALKER, R. A., 1985.     Method for the isolation of highly purified Salmonella flagellins.     Journal of clinical microbiology, 22(6), pp. 1040-1044. -   NEVILLE, B. A., FORDE, B. M., CLAESSON, M. J., DARBY, T., COGHLAN,     A., NALLY, K., ROSS, R. P. and O'TOOLE, P. W., 2012.     Characterization of pro-inflammatory flagellin proteins produced by     Lactobacillus ruminis and related motile Lactobacilli. PloS one,     7(7), pp. e40592. -   NG, S. Y., CHABAN, B. and JARRELL, K. F., 2006. Archaeal flagella,     bacterial flagella and type IV pili: a comparison of genes and     posttranslational modifications. Journal of Molecular Microbiology     and Biotechnology, 11(3-5), pp. 167-191. -   WATSON, R. O. and GALAN, J. E., 2005. Signal transduction in     Campylobacter jejuni-induced cytokine production. Cellular     microbiology, 7(5), pp. 655-665.

Bacterial Growth Conditions

R. hominis A2-183^(T) (=DSM 16839^(T)=NCIMB 14029^(T)) was grown anaerobically at 37° C. in YCFA media. The culture was spun down and the pellet was resuspended in one mL of YCFA media, supplemented with 2% cysteine (w/v, Sigma-Aldrich) and 3% ascorbic acid (w/v, Sigma-Aldrich).

R. intestinalis L1-82^(T) (=DSM 14610^(T)=NCIMB 13810^(T)) was grown anaerobically at 37° C. in YCFA media. The culture was spun down and the pellet was resuspended in one mL of YCFA media, supplemented with 2% cysteine (w/v, Sigma-Aldrich) and 3% ascorbic acid (w/v, Sigma-Aldrich).

Mice

C3H/HeN and C57Bl/6 were purchased from Harlan Laboratories. GF C3H/HeN were provided and maintained in the INRA gnotobiotic rodent breeding facility at Jouy-en-Josas (ANAXEM plateform, Institut Micalis, INRA, Jouy-en-Josas, France). GF TLRSKO and wild type C57Bl/6 were provided by Andrew Gewirtz (Center for Inflammation, Immunity, and Infection and Department of Biology, Georgia State University, Atlanta, Ga. 30303, USA) and maintained in the INRA gnotobiotic rodent breeding facility at Jouy-en-Josas. Conventional TLRSKO and wild type BOY/J were provided by Adam Cunningham (MRC Centre for Immune Regulation, Institute of Microbiology and Infection, Division of Immunity and Infection University of Birmingham UK) The management and experimental procedures were approved by the respective Local Ethical Review Committees.

Animal Experiments

Germfree animal experiments were performed in the INRA gnotobiotic rodent breeding facility at Jouy-en-Josas (ANAXEM plateform, Institut Micalis, INRA, Jouy-en-Josas, France). GF C3H/HeN male mice were allocated into control (N=8) and treatment (N=10) groups and caged individually in plastic isolators. At day 0, 1 and 2, animals in the treatment group were given 100 μL of R. hominis culture by gavage, while control animals were given 100 μL YCFA media. Ileum, ascending colon and caecum samples were collected at 14d and 28d.

Six GF C3H/HeN male mice were treated with E. coli MG1655 (1(12) as described above, and three animals were sacrificed at 10d and 22d to give N=3. Three GF TLRSKO mice and three C57Bl/6 WT mice were inoculated with R. hominis culture as described above to evaluate the functional importance of R. hominis flagellins. After 28d these animals were sacrificed together with their GF counterparts. Twenty-two female C57BL/6 mice were dosed daily with 50 μL of 10⁹ CFU R. hominis for 14 days. Control animals were dosed with culture medium alone. From day 8, mice were given DSS (MW 50 kDa, 30 g/1) in their drinking water for 6 days. The animals were euthanized on day 14 and tissue sampling was performed as described above.

Tissue Culture Experiments

Caco-2 (Homo sapiens epithelial colorectal adenocarcinoma cells) and HT29 (Homo sapiens colorectal adenocarcinoma) cells were grown in transwell plates within an anaerobic workstation. R. hominis A2-183 culture or R. intestinalis L1-82^(T) was harvested at exponential phase, and 100 μL of bacterial suspension (10⁸ CFU/mL) was added to experimental wells. Bacterial (non-adherent and adherent) and eukaryotic cells (Caco-2 and HT-29) were harvested after 2 h and 4 h incubation and stored in RNAlater. For tissue culture experiments with recombinant flagellins, 5×10⁴ Caco-2 cells were grown in 24-well plates at 37° C. in a 75% humidified atmosphere of 5% CO2. The cells reached confluence on day 5-6 and were used three days post-confluence. The cells were incubated with recombinant flagellins at a final concentration of 100 ng/μ1 for 2 hr at 37° C. in a 75% humidified atmosphere of 5% CO2.

FISH Analysis

FISH analysis was performed on neutral buffered formalin-fixed gut tissue sections using a general bacterial probe Eub338 and a newly designed R. hominis A2-183-specific probe and a R. intestinalis L1-82^(T) specific probe.

R. hominis Library Construction

R. hominis chromosomal DNA for small-size library construction and pyrosequencing was isolated using an UltraClean™ Microbial DNA Isolation Kit (Mo Bio Laboratories Inc) and high-molecular-weight DNA for fosmid libraries was isolated using a Wizard Genomic DNA Purification kit (Promega).

Microarray Analyses Bacterial Microarray

Bacterial RNA was isolated from mouse caecum contents and further processed using commercial kits following the manufacturer's recommendations. PCR products amplified from 6000 clones in the E. coli plasmid library of R. hominis were arrayed in duplicate on aminosilane-coated microscope slides (Corning) using a MicroGrid II TAS (BioRobotics).

Mouse Microarray Analysis

Total RNA was extracted from ileum and ascending colon tissue, processed into biotin-labelled cRNA/aRNA (depending on Affymetrix kit used), and hybridized to the GeneChip NuGO Mouse Array and GeneChip Mouse Genome Array (Affymetrix) using standard techniques. Data analysis was performed with the software packages R and Bioconductor.

RT-PCR Analysis

The R. hominis-specific primers 5′-CCCACTGACAGAGTATGTAATGTAC-3′ (SEQ ID NO: 14) and 5′-GCACCACCTGTCACCAC-3′ (SEQ ID NO 15) were used for PCR analysis of faecal samples to validate gut colonization levels. Real-time PCR analysis was performed using a 7500 Fast Real-Time PCR System (Applied Biosystems) with the Power SYBR Green PCR Master Mix (Applied Biosystems). All samples were run in triplicate. GyrA was used as a reference gene for normalization. For host gene expression, total eukaryotic RNA isolated from the ileum and ascending colon was reverse-transcribed into cDNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems). Real-time PCR analysis was performed using a 7500 Fast Real-Time PCR System (Applied Biosystems) with the QuantiFast SYBR Green PCR Kit (Qiagen) and QuantiTect Primer Assays (Qiagen). All samples were run in triplicate. Hprt was selected as a reference gene for normalization. All RT-PCR data were analyzed on a logarithmic scale with base 2 by one-way ANOVA with a significance cut-off of P<0.05. Differences were back-transformed to calculate fold changes.

Western Blot

Immuno-purified rabbit polyclonal antibodies against Roseburia hominis FlaA1 and FlaA2 was produced as described in Duck et al. (Duck et al. 2007). For the western blot, R. hominis was grown in the presence of varying amounts (0.01 g to 1 g diet/10 mL of culture) of UV irradiated standard mouse chow for 3 hrs, filtered to remove dietary components and diluted in laemmli buffer containing 8M urea. Samples were loaded on a NuPAGE® Novex® 4-12% Bis-Tris gel (Invitrogen) and electrophoresed, followed by further processing using the WesternBreeze Chromogenic Immunodetection System (Invitrogen). FlaA1 and FlaA2 antibodies were used at 1:1000 and loading control anti-DNA gyrase A (Abcam) at 1:300, followed by alkaline phosphatase conjugated anti-rabbit. Detection was by substrate colour development relative to loading control colour development.

Immunofluorescence

Immuno-localization of R. hominis flagellin was examined in colon contents of mice using specific antisera raised against defined peptide sequences from both FlaA1 and FlaA2 flagellin proteins. Gut content smears were fixed in pre-cooled methanol, incubated with anti-FlaA1 or anti-FlaA2 rabbit antisera (CovaLabs) at 4° C. overnight and visualized using Alexa donkey anti rabbit 488 (Molecular Probes).

T cell markers were examined on sequential 8 μm cryosection. Fixed tissue sections were incubated with Ly6G-FITC, CD3-FITC, CD11b-FITC (BD Biosciences), double-labelled with FoxP3 (Abcam) and CD3-FITC (BD Biosciences) primary antibody or isospecific IgG. Sections were counterstained with DAPI and mounted with Vectashield (Vector Laboratories). For quantification of positive cells, a minimum of five fields of view from each mouse section was examined.

Cloning and Purification of Recombinant Flagellins

Flagellin genes were isolated from liquid bacterial cultures of R. hominis, R. intestinalis, S. typhimurium, S. enteritidis, Eubacterium rectale 33656 and E. coli K12 by PCR amplification and purification. Caco-2 cells were incubated with recombinant flagellins at a final concentration of 100 ng/μL for 2 h at 37° C. in a 75% humidified atmosphere of 5% CO2.

Isolation of Intestinal and MLN Cells

Cells were isolated from the small intestine and mesenteric lymph node as previously described with minor modifications (Monteleone et al. 2008). Briefly, cellular suspensions were incubated with 100 U/mL collagenase VIII (Sigma-Aldrich) in RPMI supplemented with 20% FBS at 37° C. for 20 min (mesenteric lymph nodes) or 1 hour (intestinal pieces). Single cell suspensions were then analyzed by flow cytometry (as described).

Generation of Bone Marrow-Derived Dendritic Cells and Cultures

Bone marrow was harvested from femur and tibia of C3H/HeN and C57B16 mice. For GMCSF-derived dendritic cells, bone marrow cells were resuspended at 1×10⁶/mL in RPMI supplemented with 10% FCS and 20 ng/mL rmGM-CSF and seeded at 10 mL/plate in 100 mm² tissue culture plates. After three days culture, loosely adherent cells were collected and replated with GM-CSF supplemented media at 1×10⁶/mL in 12 well tissue culture plates. At day 5, cells were stimulated with 100 ng/mL flagellins before being harvested on day 6. For Flt3L-derived dendritic cells, bone marrow cells were resuspended at 2×10⁶/mL in RPMI supplemented with 10% FCS and 200 ng/mL rmFlt3 and seeded at 2 mL/well in 12-well tissue culture plates. Cells were cultured for 10 days with Flt3 supplemented media added to each well on day 4. At day 9, cells were stimulated with 100 ng/mL flagellins before being harvested on day 10 and analyzed by flow cytometry.

Flow Cytometry

Single cell suspensions of lamina propria cells and dendritic cells were incubated in blocking buffer (containing serum and CD16/CD32 antibody) at 4° C. for 15 min prior to staining with specific fluorochrome conjugated antibodies. Lamina propria cells were labelling with antibodies to mouse CD4-FITC and CD25-APC (eBioscience), CD8-APC-Cy7 and CD3-PerCP (Biolegend), and B220-BV570 (BD Biosciences). Intracellular FoxP3 labelling was performed after extracellular staining and cell fixation/permeabilisation according to the manufacturer's instructions (eBioscience). GMCSF-derived dendritic cells were labelled with antibodies CD11c-PE-Cy7, CD11-PerCP Cy5, I-A/I-E-APC-Cy7, CD80-PE, CD86-APC, CD8-FITC, B220-BV570. Flt3 derived dendritic cells were labelled with CD11c-PE-Cy7-, CD11b- or Siglec-H-PerCP Cy5-, I-A/I-E-APC-Cy7, CD317-PE, CD40-APC, CD103-FITC, B220-BV570 Cells were analyzed using a FACSArria (BD Biosciences) and FlowJo software version 7.2.5.

Cytometric Bead Array (CBA)

Bone marrow cells were isolated from femur and tibia with RPMI media of C3H/HeN and C57Bl/6 mice and Flt3L-expanded as described previously. Cells were stimulated with 100 ng/mL flagellin (e.g. Roseburia flagellin) after 9 days of culture, and supernatant was collected on day 10. The experiment was performed on three separate occasions to create N=3.

CBA analysis was performed on cell supernatants using the Cytometric Bead Array Mouse Enhanced Sensitivity Master Buffer Kit (BD Biosciences). Standards and samples were loaded onto a 96-well plate for measurement in a FACSArray (BD Biosciences). Results were analyzed using BD FCAP software (BD Biosciences).

Histology

Ascending colon tissue samples were fixed in neutral buffered formalin (Sigma), embedded in cold-curing resin, and 4 μm tissue sections were stained using standard haemotoxylin/eosin methods. A complete transverse cross sectional area of colon from each animal was imaged at ×200 magnification on a Zeiss Axioskop microscope using a Qlmaging camera controlled by Image Pro Plus software. Each field of view was then scored from 0-4 according to a method based on Berg et al. (Berg et al. 1996). The mean percentage of fields of view at a given grade was calculated and treatment groups were compared using student t-test analysis.

Further detailed protocols are described in the supplementary Materials and Methods.

Supplementary Information (SI) Materials and Methods Bacterial Growth Conditions

R. hominis A2-183^(T) (=DSM 16839^(T)=NCIMB 14029^(T)) was grown anaerobically on synthetic YCFA or complex M2GSC media. Culture was inoculated from frozen stock into Hungate tubes and incubated overnight at 37° C. Bacteria were then grown on M2GSC agar plates for 48 h in a MACS-MG-1000 anaerobic workstation (Don Whitley Scientific) under 80% N₂, 10% CO2, and 10% H₂ at 37° C. The effect of mucin was investigated by adding 0.5% (w/v) mucin from porcine stomach type III (Sigma-Aldrich) to the YCFA medium.

For colonization of germfree (GF) mice, R. hominis was grown in YCFA media overnight at 37° C. The culture was spun down and the pellet was resuspended in one mL of YCFA media, supplemented with 2% cysteine (w/v, Sigma-Aldrich) and 3% ascorbic acid (w/v, Sigma-Aldrich).

Mice

C3H/HeN and C57Bl/6 were purchased from Harlan Laboratories. Mice were housed within HEPA-filtered flexi-film isolators (Bell Isolation Systems) at the University of Aberdeen. GF C3H/HeN were provided and maintained in the INRA gnotobiotic rodent breeding facility at Jouy-en-Josas (ANAXEM plateform, Institut Micalis, INRA, Jouy-en-Josas, France). Germfree TLRSKO and wild type C57Bl/6 were provided by Andrew Gewirtz (Center for Inflammation, Immunity, and Infection and Department of Biology, Georgia State University, Atlanta, Ga. 30303, USA) and maintained in the INRA gnotobiotic rodent breeding facility at Jouy-en-Josas. The management and experimental procedures were approved by the respective Local Ethical Review Committees.

Mouse Experiments

Eighteen GF C3H/HeN male mice were allocated into control (N=8) and treatment (N=10) groups and caged individually in plastic isolators. The mice were fed ad libitum on a sterilized commercial diet (R03-40; UAR). At day 0, 1 and 2, animals in the treatment group were given 100 μL of R. hominis culture by gavage, while control animals were given 100 μL YCFA media. At 14d and 28d, four control animals and five R. hominis-treated animals were sacrificed. The ileum and ascending colon were divided into four equal parts and transferred to RNAlater (Ambion), neutral buffered formalin (NBF; Sigma-Aldrich) or liquid nitrogen. The whole caecum was transferred to RNAlater.

To demonstrate the specificity of the response to R. hominis, six GF C3H/HeN male mice were treated with E. coli MG1655 (K12), and three animals were sacrificed at 10d and 22d as described above to give N=3.

Three GF TLR5KO mice and three C57Bl/6 WT mice were inoculated with R. hominis culture as described above to evaluate the functional importance of R. hominis flagellins. After 28d these animals were sacrificed together with their GF counterparts.

Twenty-two female C57BL/6 mice (6 weeks old) were used to evaluate the therapeutic effect of R. hominis during DSS-induced colitis. After an acclimatization period of 7-10 days, the mice were dosed daily with 50 μL of 10⁹ CFU R. hominis for 14 days. Control animals were dosed with culture medium alone. From day 8, mice were given DSS (MW 50 kDa, 30 g/1) in their drinking water for 6 days. The animals were euthanized on day 14 and tissue sampling was performed as described above.

Tissue Culture Experiments

All cell culture reagents, unless specified otherwise, were supplied by Sigma-Aldrich. For tissue culture experiments in anaerobic conditions, 2×10⁵ Caco-2 or HT29 cells in 1.5 mL DMEM (high glucose, HEPES) medium supplemented with heat-inactivated fetal bovine serum (Gibco), penicillin, streptomycin, amphotericin B and L-glutamine were seeded into the upper compartments of a six-well transwell plate (Corning). The lower compartments contained 3.0 mL of the same medium. Cells were incubated at 37° C. in a 5% CO2 atmosphere until three days post-confluence, washed with Hanks' solution to remove antibiotics and FCS and stepped down in DMEM supplemented with L-glutamine, sodium selenite and transferrin for 24 h without antibiotics. Transwell inserts were then transferred to an anaerobic culture box within the anaerobic workstation at 37° C. The upper compartment of each insert was filled with anaerobic DMEM cell medium, while the lower compartment was filled with oxygenated DMEM.

R. hominis A2-183 culture was harvested at exponential phase by centrifugation at 3,500×g for 5 min. The pellet was washed and resuspended in 0.8 mL anaerobic DMEM. One hundred microliters of bacterial suspension (10⁸ CFU/mL) was added to experimental wells. The control wells received the same amount of medium without bacterial cells. Additional controls included bacterial cells incubated without Caco-2 or HT29 cells. Bacterial and eukaryotic cells were harvested after 2 h and 4 h incubation. Both non-adherent and adherent bacteria were aspirated and stored in RNAlater (Ambion). The viability of R. hominis cells was tested by plating onto YCFA plates. Caco-2 cells or HT-29 cells were harvested from the wells and also stored in RNAlater.

R. intestinalis L1-82^(T) (=DSM 14610^(T)=NCIMB 13810^(T)) culture was harvested at exponential phase by centrifugation at 3,500×g for 5 min. The pellet was washed and resuspended in 0.8 mL anaerobic DMEM. One hundred microliters of bacterial suspension (10⁸ CFU/mL) was added to experimental wells. The control wells received the same amount of medium without bacterial cells. Additional controls included bacterial cells incubated without Caco-2 or HT29 cells. Bacterial and eukaryotic cells were harvested after 2 h and 4 h incubation. Both non-adherent and adherent bacteria were aspirated and stored in RNAlater (Ambion). The viability of R. intestinalis cells was tested by plating onto YCFA plates. Caco-2 cells or HT-29 cells were harvested from the wells and also stored in RNAlater.

For tissue culture experiments with recombinant flagellins, 5×10⁴ Caco-2 cells were seeded in 24-well plates in DMEM (high glucose, HEPES) medium supplemented with heat-inactivated fetal bovine serum (Gibco), penicillin, streptomycin, amphotericin B and L-glutamine at 37° C. in a 75% humidified atmosphere of 5% CO2. The cells reached confluence on day 5-6 and were used 3 days post-confluency. Prior any treatment, cells were washed twice with Hanks' Balanced Salt Solution and kept in DMEM supplemented with L-Glutamine, selenium and transferrin for 24 hours.

R. hominis Library Construction

R. hominis chromosomal DNA for small-size library construction and pyrosequencing was isolated using an UltraClean™ Microbial DNA Isolation Kit (Mo Bio Laboratories Inc) and high-molecular-weight DNA for fosmid libraries was isolated using a Wizard Genomic DNA Purification Kit (Promega). DNA integrity was checked by gel electrophoresis.

DNA was mechanically sheared using a Nebulizer Kit (Invitrogen) and fractionated by gel electrophoresis. DNA fragments of desired size were excised from the gel and purified using a Wizard® SV Gel and PCR Clean-Up System (Promega). End-repair was done with a DNA Terminator End Repair Kit (Lucigen). 1.5-3.5 kb fragments were cloned using the CloneSmart® LCAmp Kit (Lucigen) and a 4-8 kb library was constructed using the pJAZZ®-OC Vector (Lucigen). Fosmid libraries were constructed using the CopyControl™ Fosmid Library Production Kit (Epicentre Biotechnologies). Colonies were picked using an automated colony picker (BioRobotics BioPick, Genomic Solutions) and archived into 384-well microtitre plates containing 70 μL 2×LB medium supplemented with 10% glycerol and corresponding antibiotic. Cells were grown overnight at 37° C. with shaking and stored at −80° C.

Sequencing, Assembly, and Annotation

Templates for sequencing of small-size libraries were generated by PCR using one μL of clone biomass and primers SL1 and SR2 surrounding the cloning site of pSMART-LCAmp. PCR products were purified using Multiscreen PCR Clean-up filter plates (Millipore). Recombinant DNA from the pJAZZ®-OC clones was isolated using the Wizard® SV 96 Plasmid DNA Purification System (Promega). Fosmid DNA was isolated using the FosmidMAX™ DNA Purification Kit (Epicentre). End-reads of DNA fragments from R. hominis WGS libraries with different insert sizes were obtained using CEQ8000 (Beckman Coulter) and ABI 3770 (Applied Biosystems) DNA sequencers. Genomic DNA from R. hominis was also sequenced using 454 GS20 (454 Life Sciences) and 454 FLX sequencers (Roche). The Sanger and 454 data were assembled with MIRA version 3 (http://chevreux.org/projects_mira.html; (1). The RAST annotation pipeline (http://rast.nmpdr.org; (2)) was used for automatic and manual annotation of the genome and for comparative genomic analyses. The annotated genomic sequence of R. hominis A2-183 was submitted to GenBank under the accession number CP003040.

Microarray Analyses Bacterial Microarray

Bacterial RNA was isolated from mouse caecum contents using the RNeasy Mini Kit (Qiagen), and further processed with the MICROBEnrich™ Kit (Ambion), the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion), and the MessageAmp™ II-Bacteria RNA Amplification Kit (Applied Biosystems). RNA was labelled with either dCTP-Cy3 or dCTP-Cy5 during cDNA synthesis (CyScribe First Strand cDNA Labelling Kit; Amersham). Labeled products were purified using the CyScribe GFX Purification Kit (Amersham). PCR products amplified from 6000 clones in the E. coli plasmid RA8 library of R. hominis were arrayed in duplicate on aminosilane-coated microscope slides (Corning) using a MicroGrid II TAS (BioRobotics). Amplified fragments of the housekeeping genes rpoD and gyrA were randomly distributed on the array as controls. Microarray hybridization was performed in the GeneTAC hybridization station (Genomic Solutions). Dye labelling was swapped for a second hybridization, and a separate RNA purification was also labelled and hybridized twice, to ensure reproducibility and to obtain statistically significant results. In total, four slides were hybridized for each comparison, for a total of 12 hybridizing spots per amplified clone. Fluorescence was measured in two channels using a GeneTAC LS IV (Genomic Solutions) with GeneTac Integrator version 3.0.1 software. Spot intensities were log-transformed and Loess normalization was applied to remove differences in probe labelling and hybridization efficiencies. The one-sample t-test was used on the log-ratio values to test for differential expression. Data was considered significant when fold change>2 and P<0.05.

(O) Mouse Microarray Analysis

Ileum and ascending colon tissue was removed from RNAlater and lyzed in Trizol (Invitrogen). RNA was isolated using standard chloroform/isopropanol steps. Total RNA was further purified with the RNeasy Kit (Qiagen), including an RNase-free DNase I (Qiagen) digestion step. RNA integrity was determined using the Agilent 2100 Bioanalyzer (Agilent Technologies). Total RNA was processed into biotin-labelled cRNA using the One-Cycle Target Labeling Kit (Affymetrix) or biotin-labelled aRNA using the 3′ IVT Express Kit (Affymetrix). Hybridization to the GeneChip NuGO Mouse Array and GeneChip Mouse Genome Array (Affymetrix) on a GeneChip Fluidics Station 450 (Affymetrix) was performed at the Institute of Medical Sciences Microarray Core Facility (University of Aberdeen, UK). Chips were scanned with an Affymetrix GeneChip Scanner 3000 (Affymetrix). Image quality analysis was performed using Gene Chip Operating Software (GCOS) (Affymetrix). Further data analysis was performed with the freely available software packages R and Bioconductor. The moderated F-test provided by the Bioconductor package limma was used to test for differential expression. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method. Statistical analysis was performed separately for each of the two time-points. All differentially expressed genes (P<0.05) were imported into MetaCore analytical software (GeneGo, St Joseph, Mich.) to generate pathway maps. Integrated pathway enrichment analysis was performed using the knowledge-based canonical pathways and endogenous metabolic pathways. Ranking of relevant integrated pathways was based onP-values calculated using hypergeometric distribution. P-values represented the probability of a given number of genes from the input list to match a certain number of genes in the map by chance, considering the numbers of genes in the experiment versus the number of genes in the map within the full set of all genes on maps.

Gene Ontology (GO) based functional interpretation of the data was performed using DAVID, an expanded version of the original web-accessible program (3). Significantly different transcripts (P<0.05) were allocated into the GO category ‘Biological Process’ to unearth patterns of gene expression significantly enriched for specific GO terms.

Microarray data were submitted to the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (accession number GSE25544).

RT-PCR Analysis

The R. hominis-specific primers 5′-CCCACTGACAGAGTATGTAATGTAC-3′ (SEQ ID NO: 14) and 5′-GCACCACCTGTCACCAC-3′ (SEQ ID NO: 15) were used for semi-quantitative and Real-time PCR analysis of faecal samples to validate gut colonization levels. Further bacterial PCR primers were designed using the on-line tool Primer3Plus (4) and purchased from Sigma-Aldrich. Real-time PCR analysis was performed using a 7500 Fast Real-Time PCR System (Applied Biosystems) with the Power SYBR Green PCR Master Mix (Applied Biosystems). PCR was performed as follows: one cycle at 95° C. for 10 min, followed by 40 cycles at 95° C. for 15 sec and 60° C. for 1 min, ending with a dissociation step. All samples were run in triplicate. GyrA was used as a reference gene for normalization due to its low variation between samples.

For host gene expression, 2 μg of total eukaryotic RNA isolated from the ileum and ascending colon was reverse-transcribed into cDNA using the High Capacity cDNA Reverse Transcription Kit (Applied Biosystems) with random primers. Real-time PCR analysis was performed using a 7500 Fast Real-Time PCR System (Applied Biosystems) with the QuantiFast SYBR Green PCR Kit (Qiagen) and QuantiTect Primer Assays (Qiagen). PCR cycling conditions were as follows: one cycle at 95° C. for 5 min, followed by 40 cycles at 95° C. for 10 seconds and at 60° C. for 30 seconds, ending with a dissociation step. All samples were run in triplicate. Hprt was selected as a reference gene for normalization because of its low variation between samples.

All RT-PCR data were analyzed on a logarithmic scale with base 2 by one-way ANOVA with a significance cut-off of P<0.05. Differences were back-transformed to calculate fold changes.

Western Blot

Immuno-purified rabbit polyclonal antibodies against Roseburia hominis Fla1 and Fla2 was produced as described in Duck et al. (5). In brief, New Zealand white female rabbits were immunized with synthetic peptide in complete Freund's adjuvant and boosted several times. For R. hominis Fla1, peptide NH2-CRSQVRGLNKASDNA-CONH₂ (SEQ ID NO: 16) and peptide NH2-IDGNFTSKKLQVGSLC-COOH (SEQ ID NO: 17) were used, while for R. hominis Fla2, peptide C-AQYNDDAKSVLEILK-COOH (SEQ ID NO: 18) and peptide C-GLNKASRNSQDGIS-CONH2 (SEQ ID NO: 19) were used. Following immunization the antibodies were purified on an immunoaffinity column prepared by coupling the peptides to 1 mL of activated sepharose beads.

For the western blot, R. hominis was grown in the presence of varying amounts (0.01 g to 1 g diet/10 mL of culture) of UV irradiated standard mouse chow for 3 hrs, filtered to remove dietary components and diluted in laemmli buffer containing 8M urea. Thirty μL of each sample was loaded into wells of a NuPAGE® Novex® 4-12% Bis-Tris gel (Invitrogen) and electrophoresed, followed by further processing using the WesternBreeze Chromogenic Immunodetection System (Invitrogen). Fla1 and Fla2 antibodies were diluted 1:1000 and loading control anti-DNA gyrase A (Abcam) diluted 1:300 in antibody diluent and incubated overnight at 4° C., followed by 1 h at room temperature with alkaline phosphatase conjugated anti-rabbit. Detection was by substrate colour development relative to loading control colour development.

FISH Analysis

Tissues fixed in neutral buffered formalin were embedded in Technovit 8100 (Heraeus Kulzer). Two-micron sections were cut using a rotary microtome (Leica/Reichert Autocut). Three sections were taken per slide at 100 μm, 200 μm and 300 μm into the tissue, resulting in nine sections per animal.

Slides were dehydrated by consecutive incubations in 50% (v/v), 80% and 96% ethanol and dried at room temperature (RT). The 16S rRNA FISH probes used were a general bacterial probe Eub338 (GCTGCCTCCCGTAGGAGT; Cy3; SEQ ID NO: 20) and a newly designed R. hominis A2-183-specific probe (GTACATTACATACTCTGTCAGTG; FITC; SEQ ID NO: 21), which was extensively tested for specificity against a panel of intestinal bacterial isolates. Ten microliter probe (30 ng/μL) in 100 μL hybridization buffer was applied to the dehydrated sample and incubated at probe-specific temperature. The slides were washed in washing buffer at 50° C. for 30 min, dipped in ice-cold water to remove residual washing buffer and dried under compressed air flow. Counterstaining was performed with 4′,6-diamidino-2-phenylindole (DAPI; Vector Laboratories Inc) and slides were mounted with Vectashield Mounting Medium for fluorescence (Vector Laboratories Inc) to prevent fading. Bacteria were visualized using a Leica DM RBE fluorescence microscope (Leitz GMBH) and photographed with a Penguin 600CL camera (Pixera) and Viewfinder 3.0 software (Studio Lite). High-magnification images (×630) were retrieved using the Apochromatics system (Leica).

Immunofluorescence

Immuno-localization of R. hominis flagellin was examined in colon contents of mice colonized with R. hominis using specific antisera raised against defined peptide sequences from both Fla1 and Fla2 flagellin proteins. Gut contents were diluted in PBS, smeared on glass slides and air dried. Smears were fixed in pre-cooled methanol for 5 min at −20° C., incubated with anti-Fla1 or anti-Fla2 rabbit antisera (1:125, CovaLabs) overnight at 4° C. and visualized using Alexa donkey anti rabbit 488 (1:1000, Molecular Probes).

Sections were fixed in pre-cooled methanol for 30 min at −20° C. Immuno-localization of T cell markers was examined on sequential cryosections (8 μm). Sections were fixed either in pre-cooled methanol for 30 min at −20° C. (Ly6G FITC, CD3 FITC, CD11b FITC, all at 1:50 (BD Biosciences)), or, for the double-labelled FoxP3 (1:500, Abcam) with CD3 FITC (1:100, BD Biosciences) fixed in 1% paraformaldehyde (PFA) for 2 min at RT followed by 3 min in 0.01% Triton X in PBS. All sections were blocked with 10% BSA (Sigma) containing 10% relevant pre-immune sera in PBS (pH 7.4). Methanol-fixed tissues were incubated with primary antibodies for 1 h at RT. PFA-fixed sections were incubated with antibodies overnight at 4° C. FoxP3 was visualized using Alexa goat anti rabbit 594 (1:1000, Molecular Probes). Sections were counter labelled with DAPI and mounted with Vectashield (Vector Laboratories). For quantification of positive cells, a minimum of five fields of view from each mouse section was examined, using imaging software and microscope settings described above.

Histology

Ascending colon tissue samples were fixed for three hours in neutral buffered formalin (Sigma) at room temperature with constant agitation. The samples rinsed in PBS and then transferred to 70% ethanol and stored at room temperature until orientated for transverse sectioning and embedded in cold-curing resin using Technovit 8100 (Heraeus Kulzer) according to the manufacturer's instructions. The embedded tissue was mounted onto Histoblocs using Technovit 3040 (Heraeus Kulzer). Four micron sections were cut using a rotary microtome (Leica Autocut) fitted with a glass knife (TAAB Laboratories Equipment Ltd.). Tissue sections were stained using standard haemotoxylin/eosin methods. A complete transverse cross sectional area of an ascending colon from each animal was imaged at ×200 magnification on a Zeiss Axioskop microscope using a QImaging camera controlled by Image Pro Plus software. Each field of view was then scored from 0-4 according to a method based on Berg et al. (6). Histopathology scores were 0=Shallow crypts, no or few infiltrating inflammatory cells, intact epithelium, goblet cells appear full of mucin (no pathology); 1=Crypts may exhibit slight epithelial cell hyperplasia, some diffuse infiltrating inflammatory cells may be seen between crypts, luminal epithelium appears intact, goblet cells may appear slightly depleted of mucin; 2=Crypts appear deeper with distinct evidence of epithelial hyperplasia, depletion of mucin from goblet cells, infiltrating inflammatory cells evident and may be multifocal in nature, although infiltrates are not seen in the submucosa; 3=Lesions involve a larger area of the mucosa and/or are more frequent than seen in grade 2. Lesions do not involve the submucosa. Luminal epithelial cells exhibit small erosions. The lesions are not transmural; 4=Crypt epithelium appears eroded. Abscesses may be present. Luminal epithelial cells appear irregular, sometimes with complete loss. Transmural infiltrate is observed—often associated with complete loss of epithelial cells into the lumen.

The mean percentage of fields of view at a given grade was calculated and treatment groups were compared using student t-test analysis.

Cloning and Purification of Recombinant Flagellins

Flagellin genes were isolated from liquid bacterial cultures of R. hominis, R. intestinalis, S. typhimurium, S. enteritidis, Eubacterium rectale 33656 and E. coli K12 by PCR amplification and purification. The purified flagellin fragment from R. hominis was inserted into expression vector pT7-MAT-Tag-FLAG (Sigma) and flagellin fragments from S. enteritidis and E. coli K12 were inserted into expression vector pGEX-6P-1 (GE Healthcare). Recombinant flagellin was expressed by transformation of plasmid DNA into E. coli BL21 Rosetta and E. coli BL21 (DE3) cells, respectively and induction with 1 mM IPTG (isopropyl b-D-galactosidase). Flagellins were recovered from cell lysates with FLAG beads (Sigma) and Ni-NTA (nickel-nitriloacetic) beads (Clontech, Takara) as per the manufacturer's instructions. The purity of the preparation was assessed by SDS-PAGE stained with coomassie blue solution. Activity of the flagellins fragments was determined by Luciferase Assay (Promega) according to the manufacturer's instructions using the NF-κB transformed Caco-2 cell line.

Caco-2 cells were incubated with recombinant flagellins at a final concentration of 100 ng/μL for 2 h at 37° C. in a 75% humidified atmosphere of 5% CO2. After the treatment the cells were washed with PBS solution twice and harvested for total RNA isolation.

Isolation of Intestinal and MLN Cells

Cells were isolated from the small intestine and mesenteric lymph node as previously described with minor modifications (7). Briefly, cellular suspensions were incubated with 100 U/ml collagenase VIII (Sigma-Aldrich) in RPMI supplemented with 20% FBS at 37° C. for 20 min (mesenteric lymph nodes) or 1 hour (intestinal pieces). Single cell suspensions were then analyzed by flow cytometry.

Generation of Bone Marrow-Derived Dendritic Cells and Cultures

Bone marrow was harvested from femur and tibia of C3H/HeN and C57B16 mice as previously described (8-11). For GMCSF-derived dendritic cells, bone marrow cells were resuspended at 1×10⁶/mL in RPMI supplemented with 10% FCS and 20 ng/mL rmGM-CSF and seeded at 10 mL/plate in 100 mm² tissue culture plates. After three days culture, loosely adherent cells were collected and replated with GM-CSF supplemented media at 1×10⁶/mL in 12 well tissue culture plates. At day 5, cells were stimulated with 100 ng/mL flagellins before being harvested on day 6. For Flt3L-derived dendritic cells, bone marrow cells were resuspended at 2×10⁶/mL in RPMI supplemented with 10% FCS and 200 ng/mL rmFlt3 and seeded at 2 mL/well in 12-well tissue culture plates. Cells were cultured for 10 days with an additional 2 mL of Flt3 supplemented media added to each well on day 4. At day 9, cells were stimulated with 100 ng/mL flagellins before being harvested on day 10. Cells were harvested from plates by gentle pipetting and analyzed by flow cytometry.

Flow Cytometry

Single cell suspensions of lamina propria cells, mesenteric lymph node cells and dendritic cells were incubated in blocking buffer (containing serum and CD16/CD32 antibody) at 4° C. for 15 min prior to staining with specific fluorochrome conjugated antibodies. Lamina propria cells were labelled with antibodies to mouse CD4-FITC and CD25-APC (eBioscience), CD8-APC-Cy7, CD3-PerCP Cy5.5 and B220-BV570 (Biolegend). Intracellular FoxP3-PE (eBioscience) labelling was performed after extracellular staining and cell fixation/permeabilisation according to the manufacturer's instructions (eBioscience). GM-CSF derived dendritic cells were labelled with antibodies CD11b-PerCP Cy5.5 (BD Biosciences), CD11c-PE-Cy7, I-A/I-E-APC-Cy7, CD80-PE, CD86-APC, CD8-FITC, B220-BV570 (Biolegend). Flt3L derived dendritic cells were labelled with CD11c-PE-Cy7-, CD11b- or Siglec-H-PerCP Cy5.5 (Bioegend), I-A/I-E-APC-Cy7, CD317-PE, CD40-Alexa Fluor 647, CD103-FITC, B220-BV570. Cells were analyzed using a FACSAriaII (BD Biosciences) and FlowJo software version 7.2.5.

Cytometric Bead Array (CBA)

Bone marrow cells were isolated from femur and tibia with RPMI media of C3H/HeN and C57Bl/6 mice and Flt3L-expanded as described previously. Cells were stimulated with 100 ng/mL flagellin (e.g. Roseburia flagellin) after 9 days of culture, and supernatant was collected on day 10. The experiment was performed on three separate occasions to create N=3.

CBA analysis was performed on cell supernatants using the Cytometric Bead Array Mouse Enhanced Sensitivity Master Buffer Kit (BD Biosciences) according to the manufacturer's instructions. Standards and samples were loaded onto a 96-well plate for measurement in a FACSArray (BD Biosciences). Results were analyzed using BD FCAP software (BD Biosciences).

Dry Body Weight and Lipid Carcass Analysis

Eviscerated mouse carcass was weighed, lyophilized to constant weight and then milled for analysis. Lipid content was determined by extraction (1:100 w/v) with chloroform/methanol (2:1 v/v) as described previously (12).

(P) Cloning of Roseburia Flagellins.

(Q) Amplification by PCR of the Flagellin Gene from Liquid Bacteria Culture.

Roseburia hominis A2-183 flagellin sequences were retrieved from the National Center for biotechnology Information (NCBI) website.

Roseburia intestinalis L1-82^(T) (NCIMB=13810; DSM=14610^(T)) flagellin sequences were retrieved from the National Center for biotechnology Information (NCBI) website. Accession numbers for the flagellin genes and proteins are provided in Table B (Table B—summary of the accession numbers for Roseburia flagellins described herein) ***

(R) Total RNA Isolation from Bacteria

Total RNA was isolated from 1 mL of log phase bacteria liquid culture using the RNAeasy minkit (Qiagen, Sussex, UK), coupled to RNase-free DNase I (Qiagen) digestion and based on manufacturer's protocol. In brief, one milliliter of liquid culture was place in a 1.5 mL tube, centrifuged at 5.000×g for 5 min at 4° C. and the supernatant was discarded. The bacterial pellet was resuspended in 100 μL of lysozyme-containing TE buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) and incubated at RT (room temperature). Gram-positive bacteria RH (Roseburia hominis) was incubated for 10 min with a lysozyme concentration of 3 mg/mL. Three hundred and fifty microliters of lysis buffer containing 1% β-mercapto-ethanol were then added to the tube to disrupt the cells by vortexing and 250 μL of 100% ethanol (Molecular grade, Merck) were added. Seven hundreds microliters of the resulting suspension was applied to the RNeasy mini column fitted with a catching tube, centrifuged for 15 seconds at 8.000×g and the catch emptied. Again, 350 μL of wash buffer was applied to the column, which was centrifuged for 15 s at 8.000×g and the flow-through discarded. DNA digestion was carried out by adding to each column, 30 units of DNase I mixed with 70 μL of RDD buffer, and incubating at RT for 15 min. The column was washed again as previously described with 350 μL of wash buffer, then twice with 500 μL of RPE buffer. After air-drying the column by centrifugation of the empty column for 1 min at 8.000×g, 40 μL of RNase-free water were added directly onto the column and incubated 1 min at RT to be centrifuged for 1 min at 8.000×g. The eluate containing the total RNA was measured spectrophotometrically using Nanodrop technique to determine the concentration. RNA integrity was checked by the RINH genomic department (University of Aberdeen, UK) with an Agilent 2100 Bioanalyzer (Agilent Technologies). RNA with integrity number (RIN) was between 9.5 and 10 was considered excellent quality. Total RNA was stored at −80° C. until later use.

(S) Reverse Transcription

Total RNA was reverse transcribed using the Quantitect reverse Transcription kit (Qiagen), according to the manufacturer's instructions. Briefly, one microgram of total RNA in a total volume of 12 μL was incubated for 2 min at 42° C. with 1×gDNA wipeout buffer and further mixed with 1× Quantiscript RT buffer (3 μL), RT primer mix (2 μL) and Quantiscript reverse transcriptase (1 μL) in a final volume of 20 μL. The reverse transcription program was 15 min at 42° C. followed by 3 min at 95° C. to inactivate the enzyme. The resulting complementary DNA (cDNA) concentration was 50 ng/0_, and the cDNA was stored at −20° C. until later use.

PCR Amplification of Flagellin Genes To amplify the flagellin from genomic DNA, forward and reverse primers were manually designed and purchased to Sigma-Aldrich (Poole, UK). The amplification by PCR of flagellin fragments was performed with forward primer inserting a BglII restriction site at 5′ end, and reverse primer inserting a XhoI restriction at the 3′ end.

Roseburia hominis (fla1) Forward primer (5′-3′):  (SEQ ID NO: 22) CTCGAGATATGGTAGTACAGCACAA Reverse primer (5′-3′):  (SEQ ID NO: 23) CTTAGATCTCTGTAATAAGGATAATA Roseburia hominis (fla2) Forward primer (5′-3′):  (SEQ ID NO: 24) CTCGAGATATGGTGGTTAATCATAA Reverse primer (5′-3′):  (SEQ ID NO: 25) CTTAGATCTTTTCAAAATCTCAAGCAC Roseburia intestinalis (Flal) Forward primer (5′-3′):  (SEQ ID NO: 26) GCAGGATCCATGCGTGGCGGAGACAAT Reverse primer (5′-3′):  (SEQ ID NO: 27) AATGTGGTGGTGGTGGTGGTGCTGCAGAATCTGCAA Roseburia intestinalis (Fla2) Forward primer (5′-3′):  (SEQ ID NO: 28) CTCGAGATATGGTAGTTAATCATAA Reverse primer (5′-3′):  (SEQ ID NO: 29) CTTAGATCTTTTTAACATTTCCAACAC Roseburia intestinalis (Fla3) Forward primer (5′-3′):  (SEQ ID NO: 22) CTCGAGATATGGTAGTACAGCACAA Reverse primer (5′-3′):  (SEQ ID NO: 30) CTTAGATCTCTGTAACAGAGAAAGTA Roseburia intestinalis (Fla4) Forward primer (5′-3′):  (SEQ ID NO: 31) CCGGGATCCATGGTAGTACAGCACAAT Reverse primer (5′-3′): (SEQ ID NO: 32) TTAGTGGTGGTGATGATGATGCTGTAACAGAGAAAG

Using 1 μL of bacterial culture as a template, the flagellin genes were amplified by PCR. The thermal program for amplification was adapted from Fermentas (Fermentas GMBH, Germany) for optimum KOD polymerase (Novagen, Madison, Wis.) functions and was 95° C. for 2 min for polymerase activation followed by 34 cycles of amplification, 95° C. for 20 s, annealing temperature for 10 s and 70° C. for 20 s ending with 2 min at 70° C. using KOD polymerase. The details of the PCR mix are given in Table 1. The PCR products were run on a 1% agarose gel for 30 min at 120 V and the bands of interest were excised and purified. The insert was first cloned into the cloning vector pCR™-Blunt II-TOPO using Zero Blunt TOPO PCR cloning kit (Invitrogen) according to the manufacturer's instructions and by mixing as described in FIG. 14 and Table 1.

TABLE-US-00019 Table 1 Composition of the mix for the insertion of PCR product into pCR-Blunt II-TOPO cloning vector. Salt solution and vector-enzyme mix were ready-to-use solutions. Components Volume (μL) PCR product 2 Salt solution 1 H₂O 2 Vector-enzyme mix 1 Total 6

(U) Electrophoretic Separation and Purification of PCR Products.

In order to view the isolated flagellin product amplified by PCR, the PCR reaction was mixed with 1× Blue-orange loading dye (Promega) and loaded onto a 1% agarose gel (made of agarose 1% diluted in TAE buffer (40 mM Tris base, 0.1% (v/v) acetic acid, 1 mM EDTA) boiled and poured in a gel tray) containing 0.5 μg/mL of Ethidium bromide to stain nucleic acids. Samples migrated for 30 min under 120 V using TAE as running buffer. When migration was finished, the gel was visualized under ultra-violet (UV) and the product was identified using a reference standard and excised with a clean scalpel. The gel slice was then transferred into a pre-weighed eppendorf tube and its weight recorded by subtraction from the empty tube weight. The PCR product was purified. Membrane binding solution was added to the gel slice in a ratio of 10 μL of solution per 10 mg of agarose gel slice. The mixture was then incubated at 65° C. for 10 min with frequent vortexing until the gel slice was completely dissolved. The tube was centrifuged briefly at RT to ensure all contents were at the bottom of the tube before progressing to DNA purification. From this point onward the purification PCR involved using Wizard® SV Gel and PCR Clean-up system (Promega, Southampton, UK) according to the manufacturer's instructions. One SV minicolumn per PCR product was placed into a collection tube. The PCR product were added to the SV minicolumn assembly and incubated for 1 min at room temperature (RT). The column was centrifuged at 16.000×g for 1 min, and the flow-through discarded. The column was then washed by adding 700 μL of membrane wash solution and centrifuged for 5 min at RT. The flow-through was discarded and the assembly spun again for 1 min and dried at RT for 2 min to evaporate any residual ethanol. The column was then transferred into a fresh 1.5 mL nuclease-free tube. To recover the PCR product, 25 μL of nuclease-free water was applied to the centre of the column and DNA was eluted by 1 min incubation at RT and 1 min spin at 16.000×g. The concentration of the eluate was measured spectrophotometrically using Nanodrop (Thermo Fisher Scientific) and stored at −20° C.

(V) Digestion of the Flagellin and Expression Vector.

Two hundred microliters of freshly thawed DH5a competent cells were kept on ice and 4 μL of the PCR product mix, and left on ice for 5 min. Heat shock was performed for 1 min at 42° C. and the cells returned on ice or 5 min, before addition of 400 μL of SOC medium. SOC Medium (Sigma) is a rich media used primarily in the recovery step of Escherichia coli competent cell transformations. Use of SOC maximizes the transformation efficiency of competent cells.

The cells grew at 37° C. for 1 hour, and 200 μL of the mix was plated on LB agar plate supplemented with Kanamycin 50 μg/mL. The positive clones were prepared as minipreps, nanodropped and digested with BamH1 and Xho1 for 2 hours to excise the flagellin. The expression vector pT7-MAT-Tag-FLAG-2 (Sigma), depicted in FIG. 2A, was also digested with BamH1 and Xho1. After separation of the product on a 1% agarose gel and purification of the digested vector and fragment i.e. the vector and the insert were ligated at 4° C. overnight and transformed into E. coli DH5a. Ligation products were plated on LB agar supplemented with ampicillin 100 μg/mL. Positives clones were prepared as minipreps and transformed into E. coli BL21 (DE3) competent cells. The positives colonies were sequenced with appropriate primers to check the presence of the insert. Glycerol aliquots were made out the positive clones. The expression vectors encoding Roseburia flagellins were further prepared as minipreps and transformed into E. coli competent cells to improve the yield of the purification; for Rh1, Rh2 and Ri2 the E. coli competent cells were E. coli BL21 Rosetta and for RI3, Ri1 Ri4, Se, St, K12, and Er the E. coli competent cells were E. coli BL21 (DE3).

(W) Expression and Purification of Roseburia Flagellins

The transformed E. coli (e.g. BL21 Rosetta) encoding the flagellin gene (RH1 or FLaA1) were grown in 1 liter LB medium with ampicillin (100 μg/mL), and supplemented with chloramphenicol (50 μg/mL) for Rosetta cells, at 37° C. under shaking 180 rpm until log phase. The culture was induced for 3 hours with 1 mM IPTG under the same conditions, to allow the specific expression of flagellin protein. Bacteria were pelleted by centrifugation 4.000×g, 4° C., for 10 min and resuspended in 60 mL of buffer 1 (50 mM Tris (pH 7.4), 150 mM NaCl) and sonicated with a Soniprep 150 (Sanyo, Japan), for 1 min when using BL21 (DE3), or 3 min when using Rosetta with 1 min rest after each minute. Cell lysate was centrifuged at 9.000×g for 10 min at 4° C. and the supernatant discarded. The pellet, which contains insoluble proteins was resuspended in 60 mL of buffer 2 (50 mM Tris (pH 8.0), 100 mM NaCl, 5 mM EDTA, 0.5% Triton-X100, 1 mM DTT) sonicated again until complete resuspension, and centrifuged at 5.000×g for 15 min at 4° C. The insoluble fraction was washed a second and a third time with buffer 2. A last wash was carried out using buffer 2 without Tx-100 and DTT, as described above. To solubilise the proteins, the insoluble fraction was resuspended using sonication in 4 mL of urea buffer (2 M urea, 50 mM Tris (pH 7.4), 150 mM NaCl) and centrifuged at 5.000×g, 5 min at RT. The supernatant was discarded by decanting and the pellet was resuspended in 2 mL of 4 M urea, 50 mM Tris (pH7.4), 150 mM NaCl by sonication and centrifuged at 5.000×g, 5 min at RT. The supernatant was collected by decanting and the pellet was resuspended in 2 mL of 8 M urea, 50 mM Tris (pH7.4), 150 mM NaCl solution by sonication and centrifuged at 5.000×g, 5 min at RT. The supernatant was collected by decanting and mixed to the 4M urea fraction, to make a 6M urea solution containing solubilized flagellins. One milliliter of Talon resin (Clontech, Takara, UK) was washed twice with 2 mL of buffer 1 (50 mM Tris (pH7.4), 150 mM NaCl) and centrifugated at 1.000×g, 2 min at RT. The supernatant was discarded and the 6 M urea fraction containing flagellin was added, and left for rotation at 4° C. for 1 hour. After centrifugation at 1.000×g for 2 min at RT, the resin was washed twice with buffer containing 2 M urea, 50 mM Tris (pH 7.4), 150 mM NaCl, 15 mM immidazole. After centrifugation, the resin was incubated for 10 min with 300 μL of elution buffer (360 mM Tris-HCl, 680 mM imidazole, 360 mM NaCl, 0.35 N HCl, 1.43 M urea), gently mixed, and the eluate was collected after centrifugation at 2.000×g for 2 min at RT. The elution was repeated once and the two eluates mixed. A second purification step using anti-FLAG M2 magnetic beads (Sigma) was performed to improve the purity of the protein preparation. Four hundred microliters of ultra pure water were slowly added to the eluate of the Talon resin, to obtain a final concentration of 0.9 M urea, suitable for FLAG beads. Two hundred fifty microliters of FLAG magnetic beads were washed twice with 750 μL of buffer 1, by mixing and leaving on a magnetic stand (Ambion) to remove the supernatant. The Talon-eluate was added to the beads and rotated for 30 min at 4° C. The beads were washed five times with 1 mL of 0.9 M urea, 50 mM Tris (pH7.4), 150 mM NaCl. The elution consisted in adding to the beads 250 μL of 200 μg/mL FLAG peptide solution containing 0.9 M urea, 50 mM Tris (pH7.4), 150 mM NaCl, mixing well and incubating 30 min at RT. The tubes were placed on the magnetic stand and the final product was collected. This elution step was repeated once and 500 μL final products were further dialyzed in PBS with 0.9 M urea for 1 hour at 4° C., prepared as aliquots and stored at −80° C. The purity of the preparations was assessed by SDS-PAGE stained with coomassie blue solution (FIG. 3A). Just before use, the protein aliquot was dialyzed 1 hour against PBS, changing the buffer twice, in slide-a-lyser of 20 kDa molecular weight cut off (Pierce, UK) and the protein concentration was measured using Bradford's method. Endotoxin measurement confirmed values were <0.25 EU/mL.

The nucleotide sequence encoding Fla1 is shown in SEQ ID NO 1 and the amino acid sequence of Fla1 is shown in SEQ ID NO 2.

TABLE-US-00020  (SEQ ID NO 1) ATGGTAGTACAGCACAATCTTACAGCAATGAACGCTAACAGACAGTTAGG TATCACAACAGGCGCACAGGCTAAGTCTTCTGAGAAGTTATCTTCTGGTT ACAAGATCAACCGCGCAGCAGATGACGCAGCAGGTCTTACGATTTCCGAG AAGATGAGAAGCCAGGTTAGAGGCTTAAATAAAGCTTCTGACAACGCACA GGATGGTGTATCCCTTATTCAGGTAGCTGAGGGTGCATTAAGTGAGACAC ACTCCATCTTACAGCGTATGAATGAGTTAGCAACTCAGGCAGCAAACGAT ACCAATACAACCTCAGACAGAACTGCAGTTCAGCAGGAGATCAACCAGTT AGCATCTGAGATCACCAGAATCGCTTCTACAACTCAGTTCAACACAATGA ACCTGATCGATGGTAACTTCACAAGTAAGAAGCTTCAGGTAGGTTCCCTT TGCGGACAGGCTATCACAATCGATATCTCTGATATGTCTGCTACAGGTCT TGGCGTTAGCGGATTAGTAGTATCTTCCTTCTCTGCAGCTGGTAAGGCAA TGTCTGCAGCTCAGGATGCTATCAGCTACGTATCTTCTATGCGTTCTAAG CTGGGTGCATTACAGAACAGACTTGAGCACACAATCTCCCACCTGGACAA CATTTCTGAGCACACATCTTCTGCAGAGTCTCGTATCCGTGATACAGATA TGGCTGAAGAGATGGTTGAGTACAGCAAGAACAACATCCTTGCTCAGGCA GGACAGTCTATGCTTGCTCAGGCTAACCAGTCTACTCAGGGTGTATTATC CTTATTACAGTAA. (SEQ ID NO 2) MVVQHNLTAMNANRQLGITTGAQAKSSEKLSSGYKINRAADDAAGLTISE KMRSQVRGLNKASDNAQDGVSLIQVAEGALSETHSILQRMNELATQAAND TNTTSDRTAVQQEINQLASEITRIASTTQFNTMNLIDGNFTSKKLQVGSL CGQAITIDISDMSATGLGVSGLVVSSFSAAGKAMSAAQDAISYVSSMRSK LGALQNRLEHTISHLDNISEHTSSAESRIRDTDMAEEMVEYSKNNILAQA GQSMLAQANQSTQGVLSLLQ.

The flagellin structure consists of four domain DO, D1, D2 and D3. See FIG. 17.

D0: N-terminal α-helix starts from Gln 2 and extends up to Ser 32 (ND0). C-terminal α-helix starts from Ala 459 and extends down to Ser 491 (CD0). The spoke region, which connects D0 and D1 domains, consists of two chains (Ns and Cs), one from Ser 32 to Ala 44 and the other from Glu 454 to Ala 459. D1: N-terminal segment extends from Ala 44 to Gln 176 and the C-terminal segment from Asn 406 to Glu 454. N-terminal segment is made of an α-helix (from Ala 44 to Ala 99) (ND1a), followed up by a loop connecting to the second, shorter α-helix (ND1b) which goes down and the chain continues to two β-turns, a β-hairpin pointing down and an extended chain going up, and the rest of the chain finally goes into domain D2. The C-terminal α-helix in domain 1 (CD1) starts from Asn 406 and extends to Glu 454. Domain D0 and D1 are packed into the protofilament structure so that N-D0 is oriented to the outside and C-D0 exposed to the central channel. D2 domain comprises two segments: N-terminal segment from Lys 177 to Gly 189 and C-terminal segment from Ala 284 to Glu 405. It is made mostly of (3 strands excepting two helix 285-289 and 288-298. D3 domain comprises a central segment from Tyr 190 to Val 283. Mostly made of (3 strands with one short stretch of helical fold (199-209).

Without wishing to be bound by theory, two essential regions of flagellin protein involved in the recognition and activation of TLR5 are thought to be amino acids at positions 79-117 of SEQ ID NO 2 (N-D1 domain) and amino acids at positions 408-439 of SEQ ID NO 2 (C-D1 domain), as well as the amino acid alanine (A) at position 411 of SEQ ID NO 2, the amino acid glutamine (Q) at position 412 of SEQ ID NO 2 and the amino acid serine (S) at position 420 of SEQ ID NO 2.

Examples

R. hominis Preferentially Colonizes the Colon

C3H/HeN germfree (GF) mice were inoculated with three gavages of R. hominis on consecutive days. The inventors report the first successful mono-colonization of germfree mice with a single bacterial species from the Firmicutes phylum. Successful colonization was achieved using an inoculation medium containing 3% ascorbic acid and 2% cysteine to protect this oxygen sensitive bacterium. Analysis of gut tissue by fluorescent in situ hybridization (FISH) revealed that R. hominis colonized both the ileum and colon, but was found in much higher numbers in the colon. Bacteria were also found closely associated with the colonic mucosa (FIG. 8A). Colonization was further validated and quantified by PCR using R. hominis-specific primers with numbers approximating 1×10¹⁰ bacteria/g faeces (FIG. 8B-C). Faeces of GF animals tested negative for the presence of any bacteria.

The R. hominis Genome Reveals Unique Genes Promoting Host Interactions

The complete genome sequence of R. hominis A2-183 was generated and is represented by a single 3,592,125-bp chromosome (FIG. 1A). Automated and manual annotation of the genome using the RAST platform revealed the presence of four ribosomal operons, 66 RNAs and 3,273 predicted proteins. The largest group of genes belonged to the Subsystem Category Carbohydrates (271 genes), encoding proteins involved in carbohydrate metabolism, followed by Protein Metabolism (197) and Amino acids and Derivatives (175) (FIG. 1B). Other important functional categories included Motility and Chemotaxis (49) and Dormancy and Sporulation (12). Comparative genomic analysis established that the closest relative in terms of genomic structure and function among the complete bacterial genomes is Eubacterium rectale (Mahowald et al. 2009), which is not surprising given the close taxonomical relatedness of these organisms (Duncan et al. 2006, Aminov et al. 2006). Comparative reconstruction of the two genomes with 1,095 genes revealed that they differed by approximately 25% of the genes. In particular, these differences encompassed genes encoding important functions for interaction with the host. For example, the Motility and Chemotaxis genes encoding type IV fimbrial assembly proteins PilB and PilC were present in E. rectale but absent in R. hominis whereas flagellar basal-body rod protein FlgC, flagellar hook-basal body complex protein FliE, flagellin protein FlaB and flagellar motor switch protein FliG were unique to R. hominis (Table 51). The two bacterial genomes also differed by 42 carbohydrate genes, reflecting their divergent nutritional requirements. Interestingly, R. hominis is unique in that it expresses two flagellin genes that are both FLA type as opposed to flagellins homologous to FliC expressed by Salmonella and E. coli bacterial species.

Table S1. Comparative analysis of the R. hominis and E. rectale genomes. Comparative genomic analysis showed that Eubacterium rectale is the closest known relative of R. hominis in terms of genomic structure and function, and the two genomes differed by approximately 25% of the genes. (A) Genes present in R. hominis but absent in E. rectale and (B) genes present in E. rectale but absent in R. hominis.

TABLE-US-00021 Table S1A. Genes present in R. hominis but absent in E. rectale. Subcategory Role Amino Acids and Derivatives Alanine, serine, and glycine L-serine dehydratase, alpha subunit Alanine, serine, and glycine L-serine dehydratase, beta subunit Arginine; urea cycle, polyamines Arginine pathway regulatory protein ArgR, repressor of arg Arginine; urea cycle, polyamines NADP-specific glutamate dehydrogenase Arginine; urea cycle, polyamines Ornithine decarboxylase Arginine; urea cycle, polyamines Spermidine Putrescine ABC transporter permease Aromatic amino acids and derivatives Biosynthetic Aromatic amino acid aminotransferase alpha Branched-chain amino acids Threonine dehydratase Glutamine, glutamate, aspartate, asparagines Aspartate aminotransferase Glutamine, glutamate, aspartate, asparagine L-asparaginase Lysine, threonine, methionine, and cysteine Sulfate permease Lysine, threonine, methionine, and cysteine Lysine decarboxylase Lysine, threonine, methionine, and cysteine Adenosylhomocysteinase Lysine, threonine, methionine, and cysteine Methionine ABC transporter ATP-binding protein Lysine, threonine, methionine, and cysteine Methionine ABC transporter permease protein Lysine, threonine, methionine, and cysteine Methionine ABC transporter substrate-binding protein Lysine, threonine, methionine, and cysteine S-ribosylhomocysteine lyase Lysine, threonine, methionine, and cysteine Predicted functional analog of homoserine kinase Carbohydrates Aminosugars Beta-hexosaminidase Central carbohydrate metabolism 6-phosphogluconolactonase Central carbohydrate metabolism Aldose 1-epimerase Central carbohydrate metabolism 4-Hydroxy-2-oxoglutarate aldolase Central carbohydrate metabolism Pyruvate: ferredoxin oxidoreductase, alpha subunit Central carbohydrate metabolism Pyruvate: ferredoxin oxidoreductase, beta subunit Central carbohydrate metabolism Pyruvate: ferredoxin oxidoreductase, delta subunit Central carbohydrate metabolism Pyruvate: ferredoxin oxidoreductase, gamma subunit Central carbohydrate metabolism Malate permease Di- and oligosaccharides Beta-glucoside bgl operon antiterminator, BglG family Di- and oligosaccharides Galactose operon repressor, GalR-LacI family of Di- and oligosaccharides Galactose/methyl galactoside ABC transport system, Di- and oligosaccharides Multiple sugar ABC transporter, ATP-binding protein Fermentation Enoyl-CoA hydratase Fermentation D-lactate dehydrogenase Monosaccharides 2-dehydro-3-deoxygluconate kinase Monosaccharides 2-dehydro-3-deoxyphosphogluconate aldolase Monosaccharides 2-deoxy-D-gluconate 3-dehydrogenase Monosaccharides Alpha-glucosidase Monosaccharides Altronate hydrolases Monosaccharides Altronate oxidoreductase Monosaccharides Beta-glucuronidase Monosaccharides D-mannonate oxidoreductase Monosaccharides Mannonate dehydratase Monosaccharides Rhamnogalacturonides degradation protein RhiN Monosaccharides Uronate isomerase Monosaccharides Sugar diacid utilization regulator SdaR Monosaccharides Ribose ABC transport system, ATP-binding protein RbsA Monosaccharides Ribose ABC transport system, permease protein RbsC Monosaccharides Pyrimidine-nucleoside phosphorylase Monosaccharides Fructokinase Monosaccharides Transcriptional repressor of the fructose operon, DeoR Monosaccharides Mannose-1-phosphate guanylyltransferase Monosaccharides Mannose-6-phosphate isomerase Monosaccharides Possible alpha-xyloside ABC transporter, substrate-binding One-carbon Metabolism Serine--pyruvate aminotransferase Sugar alcohols Glycerol uptake facilitator protein Sugar alcohols Glycerol-3-phosphate ABC transporter, periplasmic glycerol-3-phosohate-binding protein No subcategory Carbon storage regulator Cell Wall and Capsule Capsular and extracellular polysacchrides D,D-heptose 7-phosphate kinase Capsular and extracellular polysacchrides GDP-L-fucose synthetase Capsular and extracellular polysacchrides dTDP-4-dehydrorhamnose 3,5-epimerase Capsular and extracellular polysacchrides Peptidoglycan N-acetylglucosamine deacetylase Capsular and extracellular polysacchrides Polysaccharide deacetylase Capsular and extracellular polysacchrides Glucose-1-phosphate thymidylyltransferase Capsular and extracellular polysacchrides Teichoic acid translocation permease protein TagG Capsular and extracellular polysacchrides dTDP-4-dehydrorhamnose reductase Capsular and extracellular polysacchrides dTDP-glucose 4,6-dehydratase Capsular and extracellular polysacchrides TRAP-type transport system, small permease component, predicted N-acetylneuraminate transporter Capsular and extracellular polysacchrides Glucose-1-phosphate cytidylyltransferase No sub category N-acetylmuramoyl-L-alanine amidase Clustering-based subsystems Chemotaxis, response regulators diguanylate cyclase (GGDEF domain) with PAS/PAC Clustering-based subsystems Stage II sporulation protein related to metaloproteases Cytochrome biogenesis Glutamate-1-semialdehyde aminotransferase Protein export? Membrane proteins related to metalloendopeptidases Protein export? NLP/P60 family protein Protein export? Peptide chain release factor 2 Protein export? hypothetical protein BH3604 No subcategory Cell division protein FtsW No subcategory FIG. 003307: hypothetical protein No subcategory SSU ribosomal protein S1p Cofactors, Vitamins, Prosthetic Groups, Pigments Coenzyme A 2-dehydropantoate 2-reductase Coenzyme A Pantothenate: Na+ symporter Fe-S clusters Iron-sulfur cluster assembly protein SufD NAD and NADP L-Aspartate dehydrogenase Pyridoxine Predicted transcriptional regulator of pyridoxine metabolism Tetrapyrroles Alpha-ribazole-5′-phosphate phosphatase No subcategory Predicted hydroxymethylpyrimidine transporter CytX DNA Metabolism CRISPs CRISPR-associated protein Cas2 DNA repair Uracil-DNA glycosylase, family 1 DNA repair Excinuclease ABC subunit A paralog of unknown function DNA repair A/G-specific adenine glycosylase DNA repair Exodeoxyribonuclease VII small subunit DNA repair Exonuclease SbcC DNA repair Exonuclease SbcD DNA repair putative ATP-dependent DNA helicase YjcD DNA replication DNA polymerase III subunits gamma and tau DNA replication DNA replication protein DnaC No subcategory DNA-binding protein HBsu Dormancy and Sporulation Spore DNA protection Small acid-soluble spore protein, beta-type SASP No subcategory Spore maturation protein A No subcategory Spore maturation protein B Fatty Acids, Lipids, and Isoprenoids Fatty acids 4′-phosphopantetheinyl transferase Triacylglycerols Lysophospholipase Triacylglycerols Lysophospholipase L2 Triacylglycerols Monoglyceride lipase Membrane Transport ABC transporters Phosphonate ABC transporter ATP-binding protein ABC transporters Phosphonate ABC transporter permease protein phnE1 ABC transporters Phosphonate ABC transporter permease protein phnE2 ABC transporters Dipeptide transport ATP-binding protein DppD ABC transporters Dipeptide transport ATP-binding protein DppF ABC transporters Dipeptide transport system permease protein DppB ABC transporters Dipeptide transport system permease protein DppC ABC transporters Dipeptide-binding ABC transporter, periplasmic substrate- No subcategory Duplicated ATPase component BL0693 of energizing No subcategory Duplicated ATPase component MtsB of energizing module of methionine-regulated ECF transporter No subcategory Substrate-specific component BL0695 of predicted ECF No subcategory Substrate-specific component MtsA of methionine-regulated No subcategory Substrate-specific component PdxU2 of predicted No subcategory Substrate-specific component ThiT of thiamin ECF No subcategory Transmembrane component BL0694 of energizing module No subcategory Transmembrane component MtsC of energizing module of Miscellaneous Plant-Prokaryote DOE project Aspartyl-tRNA(Asn) amidotransferase subunit A Plant-Prokaryote DOE project Aspartyl-tRNA(Asn) amidotransferase subunit B Plant-Prokaryote DOE project Glutamyl-tRNA(Gln) amidotransferase subunit A Plant-Prokaryote DOE project Glutamyl-tRNA(Gln) amidotransferase subunit B Plant-Prokaryote DOE project Phosphoglucosamine mutase Plant-Prokaryote DOE project Phosphomannomutase Plant-Prokaryote DOE project ABC transport system, sugar-binding protein Plant-Prokaryote DOE project Alpha-L-arabinofuranosidase II precursor Plant-Prokaryote DOE project Alpha-N-arabinofuranosidase Plant-Prokaryote DOE project Alpha-N-arabinofuranosidase 2 Plant-Prokaryote DOE project COG3533 secreted protein Plant-Prokaryote DOE project L-arabinose isomerase Plant-Prokaryote DOE project Transcriptional repressor of the arabinose operon Plant-Prokaryote DOE project rhamnogalacturonan acetylesterase No subcategory Putative activity regulator of membrane protease YbbK Motility and Chemotaxis Flagellar motility in Prokaryota Flagellar basal-body rod protein FlgC Flagellar motility in Prokaryota Flagellar hook-basal body complex protein FliE Flagellar motility in Prokaryota Flagellin protein FlaB No subcategory Flagellar motor switch protein FliG Nitrogen Metabolism No subcategory Nitrogen regulatory protein P-II No subcategory Hcp transcriptional regulator HcpR (Crp/Fnr family) Nucleosides and Nucleotides Purines Adenine deaminase Pyrimidines Uridine kinase No subcategory Ribonucleotide reductase of class III (anaerobic), large Phosphorus Metabolism No subcategory Exopolyphosphatase No subcategory Phosphate transport system permease protein PstA No subcategory Phosphate transport system permease protein PstC No subcategory Sodium-dependent phosphate transporter Potassium metabolism No subcategory Potassium voltage-gated channel subfamily KOT Protein Metabolism Protein biosynthesis Probable GTPase related to EngC Protein biosynthesis Aspartyl-tRNA(Asn) synthetase Protein biosynthesis tRNA-Ala-CGC Protein biosynthesis tRNA-Gly-CCC Protein biosynthesis tRNA-Pro-GGG Protein biosynthesis tRNA-Ser-CGA Protein biosynthesis tRNA-Ser-GGA Protein biosynthesis tRNA-Val-CAC Protein folding Foldase protein PrsA precursor Protein processing and modification [NiFe] hydrogenase nickel incorporation protein HypA Protein processing and modification [NiFe] hydrogenase nickel incorporation-associated protein RNA Metabolism RNA processing and modification Peptidyl-prolyl cis-trans isomerase RNA processing and modification Ribonuclease P protein component Transcription Predicted transcriptional regulator of cysteine synthase, Rrf2 Transcription RNA polymerase sigma factor SigV Regulation and Cell signaling Programmed Cell Death and Toxin-antitoxin YafQ toxin protein Systems No subcategory Bifunctional autolysin Atl No subcategory Cell envelope-associated transcriptional attenuator LytR- No subcategory Aromatic hydrocarbon utilization transcriptional regulator No subcategory Catabolite control protein A No subcategory Catabolite repression HPr-like protein Crh Respiration No subcategory Ferredoxin Stress Response Cold shock Cold shock protein CspG Virulence, Disease and Defense Resistance to antibiotics and toxic compounds Probable Co/Zn/Cd efflux system membrane fusion protein Resistance to antibiotics and toxic compounds Transcriptional regulator, MerR family Resistance to antibiotics and toxic compounds Heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type Resistance to antibiotics and toxic compounds Vancomycin B-type resistance protein VanW Resistance to antibiotics and toxic compounds Tetracycline resistance protein TetW

TABLE-US-00022 Table S1B. Genes present in E. rectale but absent in R hominis. Subcategory Role Amino Acids and Derivatives Arginine; urea cycle, polyamines Transcriptional regulator, MerR family, near polyamine Lysine, threonine, methionine, and cysteine Sulfate adenylyltransferase subunit 2 Lysine, threonine, methionine, and cysteine Sulfate and thiosulfate import ATP-binding protein Lysine, threonine, methionine, and cysteine Sulfate transport system permease protein CvsW Lysine, threonine, methionine, and cysteine Methionine transporter MetT Carbohydrates Aminosugars N-Acetyl-D-glucosamine ABC transport system, Di- and oligosaccharides Galactose/methyl galactoside ABC transport system, Di- and oligosaccharides Maltodextrin glucosidase Di- and oligosaccharides PTS system, maltose and glucose-specific IIB Di- and oligosaccharides PTS system, maltose and glucose-specific IIC Fermentation NADH-dependent butanol dehydrogenase A Fermentation Alcohol dehydrogenase Monosaccharides Predicted beta-xyloside ABC transporter, substrate- One-carbon Metabolism Fumarate hydratase class I, aerobic Organic acids Serine--glyoxylate aminotransferase Polysaccharides Glycogen biosynthesis protein GlgD, glucose-1- phosphate adenylyltransferase family Polysaccharides glycogen debranching enzyme-related protein Sugar alcohols Glycerol dehydrogenase Cell Wall and Capsule Gram-Positive cell wall components Cell wall surface anchior family protein Clustering-based subsystems Cell Division FIG. 001960: FtsZ-interacting protein related to cell Isoprenoid/cell wall biosynthesis: predicted penicillin-binding protein, putative undecaprenyl diphosphate phosphatase Probably organic hydroperoxide resistance Homoserine kinase related hypothetical protein No subcategory Cell division topological specificity factor MinE No subcategory Low molecular weight protein tyrosine phosphatase Cofactors, Vitamins, Prosthetic Groups, Pigments Biotin 3-ketoacyl-CoA thiolase Biotin Biotin synthase Pyridoxine 4-hydroxythreonine-4-phosphate dehydrogenase Pyridoxine Pyridoxal kinase Pyridoxine Pyridoxine biosynthesis glutamine amidotransferase, Pyridoxine Pyridoxine biosynthesis glutamine amidotransferase, Tetraoyrroles Cob(I)alamin adenosyltransferase Tetraoyrroles Uroporphyrinogen-III methyltransferase Tetraoyrroles Vitamin B12 ABC transporter, B12-binding component No subcategory Sulfur carrier protein adenylyltransferase ThiF No subcategory Thiazole biosynthesis protein ThiG No subcategory Thiazole biosynthesis protein ThiH DNA Metabolism CRISPs CRISPR-associated protein Cas7 DNA repair Recombinational DNA repair protein RecT (prophage DNA replication ATP-dependent DNA helicase RecQ Fatty Acids, Lipids, and Isoprenoids Phospholipids CDP-diacylglycerol--serine O-phosphatidyltransferase Phospholipids Diacylglycerol kinase Iron acquisition and metabolism No subcategory Sortase A, LPXTG specific Membrane Transport No subcategory Substrate-specific component FolT of folate ECF Motility and Chemotaxis Social motility and nonflagellar swimming in Type IV fimbrial assembly protein PilC Social motility and nonflagellar swimming in Type IV fimbrial assembly, ATPase PilB Nucleosides and Nucleotides Detoxification Mutator mutT protein (7,8-dihydro-8-oxoguanine- Purines Uracil-xanthine permease Purines Adenine phosphoribosyltransferase Purines Adenosine deaminase Pyrimidines Uridine phosphorylase Phages, Prophages, Transposable elements, Plasmids Phages, Prophages Phage tail length tape-measure protein Protein Metabolism Protein biosynthesis Similar to ribosomal large subunit pseudouridine Protein biosynthesis tRNA (Guanine37-N1) -methyltransferase Protein biosynthesis Alanyl-tRNA synthetase family protein Protein degradation Aminopeptidase C Protein degradation Deblocking aminopeptidase RNA Metabolism RNA processing and modification COG1720: Uncharacterized conserved protein RNA processing and modification tRNA(Ile)-lysidine synthetase Respiration Electron accepting reactions Adenylylsulfate reductase alpha-subunit Electron accepting reactions Adenylylsulfate reductase beta-subunit Electron accepting reactions Dissimilatory sulfite reductase (desulfoviridin), alpha Stress Response Osmotic stress Choline binding protein A Osmotic stress Sarcosine oxidase alpha subunit No subcategory Carbon starvation protein A No subcategory transcriptional regulator, PemK family Sulfur Metabolism No subcategory Beta-galactosidase large subunit No subcategory Beta-galactosidase small subunit Virulence, Disease and Defense Resistance to antibiotics and toxic Aminoglycoside N6′-acetyltransferase Resistance to antibiotics and toxic Cytoplasmic copper homeostasis protein cutC R. hominis Responds to the Gut Environment by Up-Regulating Motility, Mobilization and Chemotaxis Genes

To determine the genes differentially expressed by R. hominis in response to association with the host and diet, a microarray was constructed using 6,000 PCR fragments from the small-insert-size sequencing library. Subsequent Real-time PCR validation was performed on 42 differentially expressed genes (Tables S2 and S3), which cluster at specific regions of the R. hominis genome as illustrated in FIG. 1. To distinguish between the effects of gut environment and dietary components, bacterial RNA was isolated from four different experimental conditions: (i) in vivo, from the caecum of mono-associated mice; (ii) in vitro, from bacteria grown in culture media; (iii) in vitro, from bacteria grown in the presence of dietary components; and (iv) from bacteria incubated on the surface of confluent Caco-2 and HT-29 cells.

TABLE-US-00023 Table S2. Real-time PCR analysis on bacterial RNA using R. hominis specific primers. Bacterial PCR primers were designed for differentially expressed genes using Primer3Plus. All samples were run in triplicate. GyrA was used as a reference gene for normalization. Rh14 d − In Rh28 d − In In Vitro + Rh14 d − Control Rh28 d − Control Vitro + diet Vitro + diet diet − In Vitro Gene name FC P-value FC P-value FC P-value FC P-value FC P-value 3-hydroxyacyl-CoA 5.62 0.00393 8.62 0.00000 −0.85 0.69927 1.30 0.38670 6.62 0.00124 dehydrogenase Acetyl-CoA acetyltransferase 10.25 0.00304 18.27 0.00000 1.38 0.51556 2.46 0.01882 7.44 0.00048 Aldose epimerase family protein 7.20 0.00002 11.09 0.00001 22.65 0.03173 34.89 0.02105 −0.32 0.30489 ATP synthase alpha chain 1.62 0.12713 2.50 0.00003 3.25 0.00645 5.00 0.00000 −2.00 0.00147 ATP synthase alpha chain2 11.94 0.00122 5.50 0.00001 2.71 0.18580 1.25 0.72876 4.41 0.06479 ATP synthase beta chain 1.85 0.08341 3.14 0.00056 4.00 0.00397 6.80 0.00001 −2.16 0.00241 ATP synthase beta chain2 8.27 0.00058 6.13 0.00025 1.64 0.33264 1.21 0.67923 −5.05 0.01400 ATP synthase gamma chain 2.31 0.02994 3.58 0.00027 4.22 0.00238 6.52 0.00001 −1.82 0.01276 ATP synthase gamma chain2 −9.59 0.00081 −10.55 0.00013 −1.59 0.40064 −1.75 0.29398 −6.02 0.01363 Butyryl-CoA dehydrogenase 13.31 0.00166 19.32 0.00000 1.48 0.39908 2.14 0.02840 9.03 0.00039 Electron transfer flavoprotein, 6.32 0.00729 15.55 0.00000 −0.80 0.61916 1.96 0.03441 7.94 0.00030 alpha subunit Electron transfer flavoprotein, 7.94 0.00414 12.31 0.00000 1.13 0.78504 1.76 0.08347 7.00 0.00078 beta subunit Flagellar motor rotation protein −0.94 0.71937 2.37 0.00023 1.69 0.02442 4.25 0.00001 −0.56 1.00000 MotA Flagellar motor rotation protein −0.57 0.01030 1.19 0.00938 −0.75 0.14601 1.58 0.01676 −0.76 0.08011 MotB Flagellin protein FlaA1 −3.05 0.00125 −1.93 0.01193 3.13 0.01261 4.95 0.00249 −9.57 0.00079 Flagellin protein FlaA2 1.04 0.84732 −1.28 0.05814 1.45 0.29909 1.09 0.77089 −1.39 0.28105 Flagellin protein FlaA3 1.14 0.41467 1.94 0.00312 1.63 0.08606 2.77 0.00477 −1.43 0.17174 Flagellin protein flaB 1.02 0.97319 −4.99 0.00568 1.96 0.40946 −2.60 0.14359 −1.92 0.25258 Glucuronide permease −9.34 0.00001 −13.81 0.00022 −13.97 0.00001 −20.65 0.00003 −1.50 0.13959 L-threonine 3-O-phosphate 1.62 0.00963 3.70 0.00002 1.66 0.07350 3.78 0.00186 −0.98 0.92518 decarboxylase Magnesium transporter 372.00 0.00123 11.20 0.03391 4.42 0.32048 −0.13 0.18758 84.10 0.01672 Methyl-accepting chemotaxis −1.18 0.54522 −1.83 0.02731 −2.90 0.01211 −1.87 0.05778 −0.29 0.00389 protein1 Methyl-accepting chemotaxis −2.46 0.00400 −2.95 0.00154 1.48 0.10070 1.24 0.33586 −3.65 0.00043 protein2 Methyl-accepting chemotaxis 1.13 0.54189 1.86 0.04504 3.17 0.00033 5.25 0.00055 −2.81 0.00020 protein3 Methyl-accepting chemotaxis 1.33 0.01743 2.15 0.00001 1.58 0.05704 2.56 0.00396 −1.19 0.38997 sensory transducer1 Methyl-accepting chemotaxis 2.03 0.00671 2.34 0.00017 4.94 0.00007 5.71 0.00003 −2.44 0.00163 sensory transducer2 MobA/MobL family 84.83 0.00177 5.77 0.01561 3.67 0.34227 −4.00 0.29305 23.10 0.04583 protein4/putative conjugal transfer protein MobA/MobL protein1 257.93 0.00472 9.27 0.04437 8.72 0.25455 −3.19 0.50297 29.57 0.07733 MobA/MobL protein2 714.11 0.00172 11.64 0.08286 8.17 0.29225 −7.51 0.31871 87.43 0.04300 MobA/MobL protein3 362.26 0.00144 11.10 0.03880 7.77 0.27426 −4.20 0.43208 46.62 0.06260 MobA/MobL protein4 219.75 0.00147 6.52 0.08511 7.99 0.17452 −4.22 0.34388 27.49 0.04519 Oligopeptide ABC transporter, 1.26 0.49437 1.11 0.45125 1.28 0.49171 1.13 0.53525 −1.02 0.92102 periplasmic oligopeptide-binding protein oppA Oligopeptide transport ATP- −1.29 0.05256 1.08 0.40875 −1.40 0.07422 −1.00 0.98737 1.09 0.60319 binding protein oppD Osmosensitive K+ channel 3.98 0.00004 7.07 0.00000 5.58 0.00005 9.91 0.00001 −0.71 0.12049 histidine kinase KdpD Phosphate regulon sensor protein 2.73 0.00211 1.54 0.04166 3.80 0.00919 2.14 0.07191 −1.39 0.34941 PhoR Phosphoenolpyruvate 2.30 0.05000 3.22 0.00004 1.15 0.70105 1.61 0.04623 2.00 0.00988 carboxykinase [ATP] Potassium uptake protein, integral 7.74 0.00006 10.81 0.00002 50.92 0.02191 71.15 0.01638 −0.15 0.15959 membrane component, KtrB Putative conjugal transfer protein 183.02 0.00023 9.49 0.01454 8.09 0.08695 −2.39 0.44355 22.63 0.02615 MobA/MobL Pyruvate-flavodoxin −0.52 0.05848 −0.92 0.52386 −0.36 0.01504 −0.65 0.09510 1.42 0.16352 oxidoreductase RNA polymerase sigma factor for −0.76 0.02253 1.93 0.00032 −0.82 0.08962 2.08 0.00013 −0.93 0.40060 flagellar operon

TABLE-US-00024 Table S3. Index of R. hominis PCR experiments plotted on circular genome map. List of R. hominis PCR experiments as shown on the circular genome map. Exp Primer Start End Length Gene 1 gyrA-N-F 7803 7889 87 bp gyrA 2 1602-F 95664 95740 77 bp Phosphate regulon sensor protein PhoR 3 1653-F 153403 153483 81 bp Flagellin protein FlaA1 4 1686-F 189295 189382 88 bp Flagellin protein FlaA2 5 1718-F 221205 221279 75 bp Flagellin protein FlaA3 6 1735-F 250582 250674 93 bp Methyl-accepting chemotaxis protein1 7 1769-F 290546 290628 83 bp Methyl-accepting chemotaxis sensory transducer1 8 1770-F 291722 291808 87 bp Methyl-accepting chemotaxis protein2 9 1831-N-F 348711 348810 100 bp  MobA/MobL protein4 10 1842-F 364775 364851 77 bp MobA/MobL protein2 11 1867-2652-F 391044 391120 77 bp MobA/MobL family protein4/putative conjugal transfer protein 12 2055-F 600837 600928 92 bp Acetyl-CoA acetyltransferase 13 2056-F 602279 602363 85 bp 3-hydroxyacyl-CoA dehydrogenase 14 2057-F 602961 603037 77 bp Butyryl-CoA dehydrogenase 15 2058-F 604411 604504 94 bp Electron transfer flavoprotein, beta subunit 16 2059-F 605434 605516 83 bp Electron transfer flavoprotein, alpha subunit 17 129-F 653987 654066 80 bp Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein oppA 18 132-F 658435 658516 82 bp Oligopeptide transport ATP-binding protein oppD 19 805-R 934310 934406 97 bp Osmosensitive K+ channel histidine kinase KdpD 20 807-R 935306 935394 89 bp Aldose epimerase family protein 21 808-R 936111 936190 80 bp Potassium uptake protein, integral membrane component, KtrB 22 909-F 1053529 1053604 76 bp Pyruvate-flavodoxin oxidoreductase 23 1235-F 1434705 1434785 81 bp MobA/MobL protein3 24 1296-F 1495460 1495544 85 bp Methyl-accepting chemotaxis protein3 25 1297-R 1497854 1497931 78 bp L-threonine 3-O-phosphate decarboxylase 26 1335-F 1540579 1540671 93 bp Flagellar motor rotation protein MotA 27 1336-F 1541416 1541511 96 bp Flagellar motor rotation protein MotB 28 1356-F 1559143 1559227 85 bp RNA polymerase sigma factor for flagellar operon 29 3119-F 2211612 2211705 94 bp Phosphoenolpyruvate carboxykinase [ATP] 30 3117-R 2213046 2213139 94 bp Methyl-accepting chemotaxis sensory transducer2 31 1867-2652-R 2736100 2736176 77 bp MobA/MobL family protein4/putative conjugal transfer protein 32 1552M-R 2984489 2984566 78 bp Magnesium transporter 33 397-R 3153341 3153427 87 bp ATP synthase beta chain2 34 398-R 3153616 3153699 84 bp ATP synthase gamma chain2 35 399-R 3155799 3155898 100 bp  ATP synthase alpha chain2 36 404-R 3159387 3159467 81 bp Glucuronide permease 37 2399-R 3308172 3308265 94 bp Putative conjugal transfer protein MobA/MobL 38 2323-R 3366526 3366615 90 bp Flagellin protein flaB 39 2281-R 3416947 3417042 96 bp ATP synthase beta chain 40 2280-R 3418736 3418824 89 bp ATP synthase gamma chain 41 2279-R 3418857 3418942 86 bp ATP synthase alpha chain 42 641-R 3467164 3467255 92 bp MobA/MobL protein1

Fifty differentially expressed genes were identified (in vivo vs. in vitro). The most surprising discovery was the high up-regulation in vivo of genes involved in conjugation/mobilization transfer, the mobA- and mobL-like genes (FIG. 2A). The presence of such genes in the transcriptional studies was surprising as no identifiable genes were assigned to Phages, Prophages, Transposable Elements and Plasmids in the Subsystem Category feature. This difference in gene detection and allocation is likely due to the recognized limitations of the Subsystem Category annotation. The stimulatory effect of dietary compounds was much less pronounced, suggesting that the gut environment per se is a major inducer of genes involved in horizontal gene transfer.

Other gut environment-induced subsystems included Membrane Transport, in particular magnesium transport, and Motility and Chemotaxis including multiple methyl-accepting chemotaxis proteins and genes of the flagellar operon (FIG. 2B). R. hominis possesses multiple flagellin genes flaA1, flaA2, flaA3, and flaB. In the mouse gut environment, flagellin expression was verified by Western-blot and immunocytochemistry using bacteria isolated from both in vivo colonized mice and from in vitro cultures grown in the presence of diet, with specific antibodies raised against recombinant flagellin proteins FlaA1 and FlaA2 (RH1 and RH2) (FIG. 2C). This positive validation of flagellin expression in vivo is consistent with previous reports indicating that only certain subsets of Firmicutes produce flagella in vivo (Turnbaugh et al. 2008) unlike other bacterial species that actively down-regulate expression of the bacterial protein. The expression of catabolic metabolism genes in R. hominis in the gut environment was also affected by the gut environment (FIG. 2D). The genes involved included acetyl-CoA acetyltransferase, 3-hydroxyacyl-CoA dehydrogenase, butyryl-CoA dehydrogenase and phosphoenolpyruvate carboxykinase [ATP].

To further investigate the effects of host-adaptation on the R. hominis transcriptome, in vitro stimulation of human intestinal epithelial cells (Caco-2 and HT-29) was performed. This showed that the conjugation/mobilization transfer gene mobA/mobL protein1, which was induced by adaptation to the mouse gut, was also increased in both cell lines (FIG. 2E). Consistent with the in vivo data, the flagellin gene MotA was up-regulated in Caco-2 cells. Genes involved in butyrate metabolism showed differences between the two cell lines, with down-regulation seen in Caco-2 cells and up-regulation in HT-29 cells.

R. hominis Influences Host Innate Signalling Pathways Mostly in the Colon

Colonization of GF mice with R. hominis correlated with increased host gene expression, which was highest in the colon (FIG. 3A and Table S4). Differential expression was most profound at 28d after colonization, with 159 genes up-regulated and 143 genes down-regulated. The number of differentially expressed genes in the ileum at 14d was similar to the ascending colon, with 79 genes up-regulated and 119 genes down-regulated. Differential expression in the ileum was very low at 28d, consistent with reduced colonization levels. The transcriptomic response differed at the two time-points, as shown by the clear separation of significant transcripts by heatmap analysis (FIG. 3B). Positive Real-time PCR validation of Affymetrix data is shown in FIG. 3C.

Table S4. Affymetrix Data Between R. hominis Inoculated Animals and GF Animals.

Affymetrix microarray analysis was performed on RNA isolated from ascending colon and ileum tissue. Data was considered significant when P<0.05 using the Benjamini and Hochberg false discovery method. (A) Transcripts differentially expressed in the ascending colon at 14d. (B) Transcripts differentially expressed in the ascending colon at 28d. (C) Transcripts differentially expressed in the ileum at 14d. (D) Transcripts differentially expressed in the ileum at 28d.

TABLE-US-00025 Table S4A. Transcripts differentially expressed in the ascending colon at 14 d between R. hominis inoculated animals and germfree animals. ID Symbol Name FC P-value B 1424973_at Cyp3a25 Cytochrome P450, family 3, subfamily a, polypeptide 25 26.35 4.09E−05 8.91 1449375_at Ces6 Carboxylesterase 6 22.80 5.71E−16 29.28 1428400_at 2200002K05Rik RIKEN cDNA 2200002K05 gene 6.22 6.65E−09 17.20 1419393_at Abcg5 ATP-binding cassette, sub-family G (WHITE), member 5 5.81 0.002156 4.51 1429726_at Slc16a9 Solute carrier family 16 (monocarboxylic acid transporters), 4.38 0.001103 5.26 member 9 1430641_at 9030605I04Rik RIKEN cDNA 9030605I04 gene 4.36 0.000358 6.52 1436575_at Grin3a Glutamate receptor ionotropic, NMDA3A 3.91 0.018503 1.71 1422749_at Ly6g6c Lymphocyte antigen 6 complex, locus G6C 3.71 0.004044 3.79 NuGO_emt070648_at Abca12 ATP-binding cassette, sub-family A (ABC1), member 12 3.69 0.000333 6.62 1428682_at Zc3h6 Zinc finger CCCH type containing 6 3.28 0.002747 4.26 1431554_a_at Anxa9 Annexin A9 3.00 3.25E−05 9.18 1423556_at Akr1b7 Aldo-keto reductase family 1, member B7 2.87 0.018503 1.70 1424451_at Acaa1b Acetyl-Coenzyme A acyltransferase 1B 2.70 0.000404 6.33 1418486_at Vnn1 Vanin 1 2.66 0.001531 4.93 1418606_at Hoxd10 Homeo box D10 2.60 0.000102 7.97 1435207_at Dixdc1 DIX domain containing 1 2.55 0.014337 2.11 1427072_at Stard8 START domain containing 8 2.48 0.027058 1.15 1442560_at NA NA 2.42 0.006928 3.17 1420998_at Etv5 Ets variant gene 5 2.33 0.017697 1.81 1440925_at Rhoq Ras homolog gene family, member Q 2.32 0.013564 2.22 1428902_at Chst11 Carbohydrate sulfotransferase 11 2.30 0.000154 7.46 1416607_at 4931406C07Rik RIKEN cDNA 4931406C07 gene 2.28 7.26E−11 21.08 1435673_at Hoxd3 Homeo box D3 2.26 0.019944 1.60 1426663_s_at Slc45a3 Solute carrier family 45, member 3 2.21 0.007554 3.07 1419651_at 2610200G18Rik RIKEN cDNA 2610200G18 gene 2.21 0.000406 6.29 1422188_s_at NA NA 2.20 0.000397 6.39 1435468_at D230025D16Rik RIKEN cDNA D230025D16 gene 2.15 0.018503 1.71 1417991_at Diol Deiodinase, iodothyronine, type I 2.12 0.026066 1.24 1451557_at Tat Tyrosine aminotransferase 2.11 0.046376 0.38 1428989_at 0710001D07Rik RIKEN cDNA 0710001D07 gene 2.03 0.04028 0.54 1456680_at B3gnt6 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2.01 0.024447 1.35 6 (core 3 synthase) 1443235_at Eif2ak4 Eukaryotic translation initiation factor 2 alpha kinase 4 1.97 0.002156 4.51 1419759_at Abcb1a ATP-binding cassette, sub-family B (MDR/TAP), member 1A 1.97 0.009639 2.79 1456389_at Zeb2 Zinc finger E-box binding homeobox 2 1.96 0.013795 2.16 1440840_at D630004K10Rik RIKEN cDNA D630004K10 gene 1.96 0.017697 1.80 1457619_at Ces6 Carboxylesterase 6 1.94 0.04028 0.55 1449049_at Tlr1 Toll-like receptor 1 1.92 0.018503 1.72 NuGO_emt049113_at Ptprh Protein tyrosine phosphatase, receptor type, H 1.89 0.002961 4.17 1424376_at Cdc42ep1 CDC42 effector protein (Rho GTPase binding) 1 1.88 0.014337 2.10 1436566_at Rab40b Rab40b, member RAS oncogene family 1.87 0.028805 1.04 1432590_at LOC621549 NA 1.83 0.012459 2.38 1430543_at Clip3 CAP-GLY domain containing linker protein 3 1.82 6.24E−05 8.47 1435553_at Pdzd2 PDZ domain containing 2 1.81 0.048735 0.32 1428271_at Acbd4 Acyl-Coenzyme A binding domain containing 4 1.80 0.014378 2.09 1418059_at Eltd1 EGF, latrophilin seven transmembrane domain containing 1 1.79 0.005331 3.47 1456532_at Pdgfd Platelet-derived growth factor, D polypeptide 1.77 0.007554 3.05 1437393_at AI875142 Expressed sequence AI875142 1.77 0.03504 0.78 1428332_at 1500004A08Rik RIKEN cDNA 1500004A08 gene 1.77 0.038684 0.61 1434015_at Slc2a6 Solute carrier family 2 (facilitated glucose transporter), member 6 1.75 0.000437 6.19 1449403_at Pde9a Phosphodiesterase 9A 1.71 0.03504 0.79 1428260_at Spg3a Spastic paraplegia 3 A homolog (human) 1.69 0.011437 2.55 1417803_at 1110032A04Rik RIKEN cDNA 1110032A04 gene 1.66 0.001103 5.27 1430245_at Fxr1h Fragile X mental retardation gene 1, autosomal homolog 1.66 0.012459 2.36 1422542_at Gpr34 G protein-coupled receptor 34 1.65 0.031372 0.95 1427020_at Scara3 Scavenger receptor class A, member 3 1.60 0.010425 2.69 1430211_at 4930415O20Rik RIKEN cDNA 4930415020 gene 1.57 0.045 0.42 1452809_at 9030607L17Rik RIKEN cDNA 9030607L17 gene 1.53 0.013564 2.22 NuGO_emt066282_at Defb37 Defensin beta 37 1.51 0.005422 3.44 1451498_at BC004853 cDNA sequence BC004853 1.50 0.037045 0.69 1434140_at Mcf2l Mcf.2 transforming sequence-like 1.49 0.025597 1.30 1452650_at Trim62 Tripartite motif-containing 62 1.46 0.02652 1.19 1427492_at Pof1b Premature ovarian failure 1B 1.46 0.004679 3.61 1426601_at Slc37a1 Solute carrier family 37 (glycerol-3-phosphate transporter), 1.42 0.032433 0.90 member 1 1448188_at Ucp2 Uncoupling protein 2 (mitochondrial, proton carrier) 1.42 0.008209 2.96 1460409_at Cpt1a Carnitine palmitoyltransferase 1a, liver 1.40 0.025932 1.26 1460652_at Esrra Estrogen related receptor, alpha 1.39 0.038182 0.65 1453869_at LOC328277 NA 1.36 0.017271 1.86 1435985_at Farp2 FERM, RhoGEF and pleckstrin domain protein 2 1.34 0.037045 0.70 1454706_at Uvrag UV radiation resistance associated gene 1.34 0.021704 1.51 1451232_at Cdl51 CD151 antigen 1.31 0.049274 0.31 1423570_at Abcg1 ATP-binding cassette, sub-family G (WHITE), member 1 1.30 0.04028 0.55 1418817_at Chmp1b Chromatin modifying protein 1B 1.25 0.010981 2.61 1441059_at 1700049G17Rik RIKEN cDNA 1700049G17 gene 1.25 0.028805 1.05 NuGO_emt061346_at NA NA 1.24 0.026697 1.17 1420503_at Slc6a14 Solute carrier family 6 (neurotransmitter transporter), member 14 1.22 0.012499 2.32 NuGO_emt073103_x_at NA NA 1.21 0.01946 1.63 1452592_at Mgst2 Microsomal glutathione S-transferase 2 1.18 0.038684 0.60 1441135_at NA NA −1.10 0.01646 1.92 1428482_at Akap10 A kinase (PRKA) anchor protein 10 −1.20 0.022427 1.47 1426679_at Zfp706 Zinc finger protein 706 −1.26 0.028805 1.05 1415816_at Cct7 Chaperonin subunit 7 (eta) −1.26 0.011936 2.47 1445024_at Stard7 START domain containing 7 −1.27 0.03504 0.79 1453591_at 5730437N04Rik RIKEN cDNA 5730437N04 gene −1.32 0.02652 1.19 1450788_at Saa1 Serum amyloid A 1 −1.32 0.002156 4.54 1436157_at Ccar1 Cell division cycle and apoptosis regulator 1 −1.33 0.034783 0.81 1450987_a_at 2310004I24Rik RIKEN cDNA 2310004I24 gene −1.35 0.0361 0.73 1433850_at Ppp4r2 Protein phosphatase 4, regulatory subunit 2 −1.36 0.018503 1.71 1434835_at Wapal Wings apart-like homolog (Drosophila) −1.37 0.027058 1.14 NuGO_emt090017_s_at Cdk7 Cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk- −1.37 0.044186 0.44 activating kinase) 1422579_at Hspe1 Heat shock protein 1 (chaperonin 10) −1.38 0.017697 1.81 1455726_at Gm71 Gene model 71, (NCBI) −1.42 0.029302 1.02 1420461_at Mst1r Macrophage stimulating 1 receptor (c-met-related tyrosine −1.49 0.046838 0.37 kinase) 1453264_at Marveld3 MARVEL (membrane-associating) domain containing 3 −1.49 0.005522 3.40 1425030_at Zfp622 Zinc finger protein 622 −1.49 0.000586 5.89 1458507_at 2810055G22Rik RIKEN cDNA 2810055G22 gene −1.50 0.032433 0.89 1443988_at Rbm39 RNA binding motif protein 39 −1.51 0.037045 0.68 1460465_at A930038C07Rik RIKEN cDNA A930038C07 gene −1.51 0.004627 3.64 1428784_at Gmip Gem-interacting protein −1.51 0.045 0.42 1451621_at 5830417C01Rik RIKEN cDNA 5830417C01 gene −1.65 0.014536 2.07 1422837_at Scel Sciellin −1.68 0.0361 0.74 1454617_at Arrdc3 Arrestin domain containing 3 −1.71 0.038496 0.62 1452047_at Cacybp Calcyclin binding protein −1.72 0.018495 1.75 1434724_at Usp31 Ubiquitin specific peptidase 31 −1.75 0.024018 1.39 1417032_at Ube2g2 Ubiquitin-conjugating enzyme E2G 2 −1.76 0.04028 0.56 1448628_at Scg3 Secretogranin III −1.77 0.016351 1.93 1443877_a_at Rapgef6 Rap guanine nucleotide exchange factor (GEF) 6 −1.82 0.004044 3.80 1427944_at Caprin2 Caprin family member 2 −1.85 0.04248 0.49 1415909_at Stip1 Stress-induced phosphoprotein 1 −1.89 0.024018 1.38 1422452_at Bag3 Bcl2-associated athanogene 3 −1.89 0.026066 1.24 1438041_at Pde7a Phosphodiesterase 7A −1.91 0.025597 1.29 1433927_at Uspl1 Ubiquitin specific peptidase like 1 −1.92 0.024018 1.38 1422860_at Nts Neurotensin −1.94 1.84E−07 14.19 1451194_at Aldob Aldolase 2, B isoform −1.94 7.08E−06 10.59 1441662_at Cyp4x1 Cytochrome P450, family 4, subfamily x, polypeptide 1 −1.95 0.00019 7.22 1445490_at C77805 Expressed sequence C77805 −1.96 0.003479 4.00 NuGO_emt066852_at NA NA −2.07 0.013658 2.19 1442427_at NA NA −2.11 0.033207 0.86 1430185_at Akap13 A kinase (PRKA) anchor protein 13 −2.12 0.0361 0.74 1452462_a_at Banp Btg3 associated nuclear protein −2.16 0.038182 0.64 1446158_at Exoc6b Exocyst complex component 6B −2.19 0.010302 2.72 1418113_at Cyp2d10 Cytochrome P450, family 2, subfamily d, polypeptide 10 −2.24 0.012383 2.42 1426645_at Hsp90aa1 Heat shock protein 90 kDa alpha (cytosolic), class A member 1 −2.30 0.012459 2.34 1420150_at Spsb1 SplA/ryanodine receptor domain and SOCS box containing 1 −2.36 0.015257 2.01 1452382_at Dnm3os Dynamin 3, opposite strand −2.37 0.025932 1.26 1460645_at Chordc1 Cysteine and histidine-rich domain (CHORD)-containing, zinc- −2.38 0.002156 4.53 binding protein 1 1457477_at NA NA −2.39 0.027058 1.14 1430175_at Tmtc2 Transmembrane and tetratricopeptide repeat containing 2 −2.40 0.028805 1.05 1433266_at 2810416A17Rik RIKEN cDNA 2810416A17 gene −2.43 0.0361 0.73 1416756_at Dnajb1 DnaJ (Hsp40) homolog, subfamily B, member 1 −2.50 0.013658 2.19 1415938_at Spink3 Serine peptidase inhibitor, Kazal type 3 −2.53 0.012459 2.35 1429273_at Bmper BMP-binding endothelial regulator −2.53 0.012459 2.34 1450518_at Hnf4g Hepatocyte nuclear factor 4, gamma −2.53 0.019018 1.66 1440227_at BF642829 Expressed sequence BF642829 −2.58 0.038494 0.63 1451924_a_at Edn1 Endothelin 1 −2.63 0.011568 2.51 1425952_a_at Gcg Glucagon −2.65 2.76E−06 11.57 1459253_at Arrdc3 Arrestin domain containing 3 −2.69 0.026081 1.23 1416288_at Dnaja1 DnaJ (Hsp40) homolog, subfamily A, member 1 −2.75 0.000154 7.45 1435160_at 1110064P04Rik RIKEN cDNA 1110064P04 gene −2.76 0.011568 2.52 1460179_at Dnaja1 DnaJ (Hsp40) homolog, subfamily A, member 1 −2.78 0.000251 6.92 1419349_a_at Cyp2d9 Cytochrome P450, family 2, subfamily d, polypeptide 9 −2.78 0.000134 7.68 NuGO_emt044299_at Sstr1 Somatostatin receptor 1 −2.80 3.73E−07 13.38 1449493_at Insl5 Insulin-like 5 −2.91 5.33E−08 15.35 NuGO_emt054105_at D630013G24Rik RIKEN cDNA D630013G24 gene −2.99 0.004044 3.83 1419185_a_at Mlxipl MLX interacting protein-like −3.16 4.43E−06 11.08 1449939_s_at Dlk1 Delta-like 1 homolog (Drosophila) −3.29 9.19E−11 20.69 1458385_at Hspa41 Heat shock protein 4 like −3.36 0.032433 0.90 1422639_at Calcb Calcitonin-related polypeptide, beta −3.75 0.010981 2.62 1425993_a_at Hsp110 Heat shock protein 110 −4.08 0.028805 1.05 NuGO_emt091063_at NA NA −6.03 3.11E−07 13.63 1419473_a_at Cck Cholecystokinin −10.87 4.94E−11 21.66 1452388_at Hspa1a Heat shock protein 1A −25.30 0.02652 1.19

TABLE-US-0026 Table S4B. Transcripts differentially expressed in the ascending colon at 28 d between R. hominis inoculated animals and germfree animals. ID Symbol Name FC P-value B 1416809_at Cyp3a11 Cytochrome P450, family 3, subfamily a, polypeptide 11 89.84 1.45E−06 12.00 1424973_at Cyp3a25 Cytochrome P450, family 3, subfamily a, polypeptide 25 52.30 7.31E−07 12.67 1419393_at Abcg5 ATP-binding cassette, sub-family G (WHITE), member 5 42.06 1.60E−09 18.55 1449375_at Ces6 Carboxylesterase 6 26.10 1.75E−16 31.66 1422749_at Ly6g6c Lymphocyte antigen 6 complex, locus G6C 25.49 2.06E−10 20.64 1448964_at S100g S100 calcium binding protein G 17.88 4.82E−07 13.11 1455540_at Cps1 Carbamoyl-phosphate synthetase 1 11.50 0.010507 1.76 1449133_at Sprr1a Small proline-rich protein 1A 11.27 0.009303 1.97 NuGO_emt070648_at Abca12 ATP-binding cassette, sub-family A (ABC1), member 12 7.97 4.05E−08 15.43 1448485_at Ggt1 Gamma-glutamyltransferase 1 7.45 0.020934 0.94 1417828_at Aqp8 Aquaporin 8 6.67 0.001582 4.30 1437060_at Olfm4 Olfactomedin 4 5.80 0.023469 0.77 1420437_at Indo Indoleamine-pyrrole 2,3 dioxygenase 5.18 0.000637 5.44 1425452_s_at AW125753 Expressed sequence AW125753 4.97 0.001639 4.20 1439934_at Slc30a10 Solute carrier family 30, member 10 4.68 0.000119 7.49 1430641_at 9030605I04Rik RIKEN cDNA 9030605I04 gene 4.47 0.000199 6.89 1423556_at Akr1b7 Aldo-keto reductase family 1, member B7 4.36 0.000304 6.44 1428400_at 2200002K05Rik RIKEN cDNA 2200002K05 gene 4.31 4.81E−07 13.18 1424626_at 2010003K11Rik RIKEN cDNA 2010003K11 gene 4.25 0.024887 0.68 1439727_at Clca6 Chloride channel calcium activated 6 4.09 0.000869 5.07 1450355_a_at Capg Capping protein (actin filament), gelsolin-like 3.90 4.67E−05 8.59 1427119_at Spink4 Serine peptidase inhibitor, Kazal type 4 3.67 0.007507 2.25 NuGO_emt092118_s_at NA NA 3.51 0.040399 −0.04 1451239_a_at Slc26a1 Solute carrier family 26 (sulfate transporter), member 1 3.36 0.004508 2.94 1418283_at Cldn4 Claudin 4 2.97 0.002809 3.51 1418165_at Itlna Intelectin a 2.88 0.0005 5.82 1440192_at 1810054D07Rik RIKEN cDNA 1810054D07 gene 2.86 0.000108 7.65 1426980_s_at E130012A19Rik RIKEN cDNA E130012A19 gene 2.83 0.002052 3.91 1431042_at Paqr8 Progestin and adipoQ receptor family member VIII 2.67 0.000637 5.46 1424688_at Creb3l3 cAMP responsive element binding protein 3-like 3 2.67 0.035165 0.19 NuGO_emt049113_at Ptprh Protein tyrosine phosphatase, receptor type, H 2.54 6.75E−06 10.55 1432358_at Muc16 Mucin 16 2.47 0.044391 −0.20 1419759_at Abcb1a ATP-binding cassette, sub-family B (MDR/TAP), member 1A 2.46 0.00017 7.13 NuGO_emt033610_at Nox1 NADPH oxidase 1 2.43 0.035165 0.20 1418661_at Abhd2 Abhydrolase domain containing 2 2.41 0.043727 −0.17 1420499_at Gch1 GTP cyclohydrolase 1 2.38 0.040391 −0.03 1416607_at 4931406C07Rik RIKEN cDNA 4931406C07 gene 2.31 3.39E−11 22.26 1417991_at Dio1 Deiodinase, iodothyronine, type I 2.29 0.006845 2.39 1455455_at Glt28d2 Glycosyltransferase 28 domain containing 2 2.16 0.015457 1.33 1417164_at Dusp10 Dual specificity phosphatase 10 2.13 0.031006 0.40 1428937_at Atp2b1 ATPase, Ca++ transporting, plasma membrane 1 2.13 1.13E−05 9.98 1429833_at Ly6g6e Lymphocyte antigen 6 complex, locus G6E 2.10 0.042694 −0.12 1419582_at Cyp2c55 Cytochrome P450, family 2, subfamily c, polypeptide 55 2.06 0.022426 0.83 1448562_at Upp1 Uridine phosphorylase 1 2.06 0.007369 2.29 1444254_at NA NA 2.05 0.009642 1.90 1428936_at Atp2b1 ATPase, Ca++ transporting, plasma membrane 1 2.05 0.000378 6.15 1421268_at Ugcg UDP-glucose ceramide glucosyltransferase 2.05 0.035029 0.21 1419478_at Sectm1b Secreted and transmembrane 1B 2.02 0.004814 2.83 1428336_at Agpat4 1-acylglycerol-3-phosphate O-acyltransferase 4 (lysophosphatidic acid 2.02 0.047797 −0.32 acyltransferase, delta) 1456231_at Pla2g3 Phospholipase A2, group III 1.99 0.000365 6.21 1421709_a_at Fmo5 Flavin containing monooxygenase 5 1.97 0.02187 0.86 1455104_at NA NA 1.95 0.010934 1.71 1417133_at Pmp22 Peripheral myelin protein 1.95 0.027135 0.58 1418206_at Sdf2lI Stromal cell-derived factor 2-like 1 1.94 0.045914 −0.25 1436614_at AI843639 Expressed sequence AI843639 1.94 0.006795 2.41 1452070_at Dedd2 Death effector domain-containing DNA binding protein 2 1.92 0.046848 −0.28 1417404_at Elovl6 ELOVL family member 6, elongation of long chain fatty acids (yeast) 1.90 0.012549 1.55 1417277_at Cyp4f16 Cytochrome P450, family 4, subfamily f, polypeptide 16 1.87 0.000119 7.50 1422983_at Itgb6 Integrin beta 6 1.87 0.03266 0.33 1454746_at Plekhm1 Pleckstrin homology domain containing, family M (with RUN 1.86 0.001042 4.88 domain) member 1 1425079_at Tm6sf2 Transmembrane 6 superfamily member 2 1.85 0.001269 4.60 1455099_at Mogat2 Monoacylglycerol O-acyltransferase 2 1.85 0.024887 0.68 1435749_at Gda Guanine deaminase 1.82 0.002467 3.67 1416488_at Ccng2 Cyclin G2 1.81 0.003976 3.09 1418256_at Srf Serum response factor 1.79 0.033108 0.26 1426744_at Srebf2 Sterol regulatory element binding factor 2 1.76 0.041026 −0.07 1457253_at Trim40 Tripartite motif-containing 40 1.75 0.001269 4.61 1433556_at Cental Centaurin, alpha 1 1.75 0.009141 2.01 NuGO_emt084792_x_at NA NA 1.74 0.020944 0.92 1417823_at Gcat Glycine C-acetyltransferase (2-amino-3-ketobutyrate-coenzyme A 1.74 0.049235 −0.38 ligase) NuGO_emt066282_at Defb37 Defensin beta 37 1.74 6.42E−05 8.25 1429550_at Entpd8 Ectonucleoside triphosphate diphosphohydrolase 8 1.73 0.004814 2.85 1430594_at Rab11fip1 RAB11 family interacting protein 1 (class I) 1.73 0.033108 0.27 1420913_at Slco2a1 Solute carrier organic anion transporter family, member 2a1 1.73 0.001791 4.09 NuGO_emt043440_at 2210010C17Rik RIKEN cDNA 2210010C17 gene 1.73 0.01702 1.21 1430674_at 1700016C15Rik RIKEN cDNA 1700016C15 gene 1.73 0.036022 0.14 1430890_at 2210010C17Rik RIKEN cDNA 2210010C17 gene 1.72 0.011201 1.68 1417803_at 1110032A04Rik RIKEN cDNA 1110032A04 gene 1.71 0.000358 6.25 1449873_at Bmp8a Bone morphogenetic protein 8a 1.71 0.044796 −0.22 1434130_at Lhfpl2 Lipoma HMGIC fusion partner-like 2 1.71 0.004814 2.83 1448605_at Rhoc Ras homolog gene family, member C 1.70 0.001099 4.79 1432363_at 2410018E23Rik RIKEN cDNA 2410018E23 gene 1.69 0.04853 −0.34 1427878_at 0610010O12Rik RIKEN cDNA 0610010O12 gene 1.68 2.48E−05 9.21 1416379_at Panx1 Pannexin 1 1.67 0.002404 3.74 1434059_at B230312A22Rik RIKEN cDNA B230312A22 gene 1.65 0.001763 4.12 1452475_at Pcsk5 Proprotein convertase subtilisin/kexin type 5 1.65 0.036022 0.12 1454399_at 2010003H20Rik RIKEN cDNA 2010003H20 gene 1.62 0.016629 1.24 1460550_at Mtmr11 Myotubularin related protein 11 1.62 0.010762 1.73 NuGO_emt070892_at NA NA 1.62 0.020773 0.95 1436710_at Zswim4 Zinc finger, SWIM domain containing 4 1.62 0.009718 1.88 1420663_at Zbtb7b Zinc finger and BTB domain containing 7B 1.61 0.042694 −0.13 1418991_at Bak1 BCL2-antagonist/killer 1 1.61 0.01094 1.71 1417990_at Ppp1r14d Protein phosphatase 1, regulatory (inhibitor) subunit 14D 1.59 0.003746 3.16 1452837_at Lpin2 Lipin 2 1.58 0.035702 0.16 NuGO_emt021769_s_at Slc17a4 Solute carrier family 17 (sodium phosphate), member 4 1.57 0.015878 1.30 1418671_at Capn5 Calpain 5 1.57 0.041629 −0.09 1417751_at Stk10 Serine/threonine kinase 10 1.57 0.027636 0.55 1452294_at Pcdh1 Protocadherin 1 1.56 0.003042 3.42 1429154_at Slc35f2 Solute carrier family 35, member F2 1.56 0.004185 3.02 1450982_at Slc9a3r1 Solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 1.56 0.008755 2.06 regulator 1 1434015_at Slc2a6 Solute carrier family 2 (facilitated glucose transporter), member 6 1.55 0.005093 2.72 1418712_at Cdc42ep5 CDC42 effector protein (Rho GTPase binding) 5 1.55 0.003976 3.09 1424809_at Crb3 Crumbs homolog 3 (Drosophila) 1.53 0.014107 1.43 1428953_at Otud7b OTU domain containing 7B 1.53 0.035702 0.17 1424090_at Sdcbp2 Syndecan binding protein (syntenin) 2 1.53 0.023574 0.76 1418215_at Mep1b Meprin 1 beta 1.53 0.027636 0.55 1434456_at Gm440 gene model 440, (NCBI) 1.53 0.032752 0.32 1423521_at Lmnb1 Lamin B1 1.53 0.007369 2.31 1425298_a_at Naip1 NLR family, apoptosis inhibitory protein 1 1.51 0.002438 3.70 1456619_at Liph Lipase, member H 1.50 0.044796 −0.22 1418976_s_at Cideb Cell death-inducing DNA fragmentation factor, alpha subunit-like 1.49 0.020944 0.93 effector B 1423376_a_at Dok4 Docking protein 4 1.49 0.005089 2.73 1415793_at Pnpo Pyridoxine 5′-phosphate oxidase 1.48 0.00252 3.63 1435461_at Magi3 Membrane associated guanylate kinase, WW and PDZ domain 1.48 0.001623 4.23 containing 3 1444951_at BC042698 cDNA sequence BC042698 1.45 0.042694 −0.14 1452214_at Skil SKI-like 1.45 0.020383 0.99 1426284_at Krt20 Keratin 20 1.43 0.021519 0.88 1460406_at AI427122 Expressed sequence AI427122 1.42 0.016225 1.27 1419331_at Cdh17 Cadherin 17 1.41 0.009399 1.94 1428509_at Myo1e Myosin IE 1.41 0.043727 −0.17 1429117_at Tradd TNFRSF1A-associated via death domain 1.41 0.020944 0.91 1460681_at Ceacam2 CEA-related cell adhesion molecule 2 1.41 0.036022 0.14 1455678_at NA NA 1.41 0.048555 −0.36 1440218_at BC040758 cDNA sequence BC040758 1.41 0.026321 0.62 1416009_at Tspan3 Tetraspanin 3 1.40 0.002052 3.91 1456200_at Ipmk Inositol polyphosphate multikinase 1.40 0.033108 0.28 1424126_at Alas1 Aminolevulinic acid synthase 1 1.39 0.040391 −0.03 1434482_at D4Ertd22e DNA segment, Chr 4, ERATO Doi 22, expressed 1.39 0.038213 0.05 1416690_at Gtpbp2 GTP binding protein 2 1.38 0.035702 0.16 1417895_a_at Tmem54 Transmembrane protein 54 1.38 0.001332 4.53 1424245_at Ces2 Carboxylesterase 2 1.37 0.020383 0.99 1434559_at Stx3 Syntaxin 3 1.37 0.032755 0.31 1426733_at Itpk1 Inositol 1,3,4-triphosphate ⅚ kinase 1.35 0.010099 1.81 1451139_at Slc39a4 Solute carrier family 39 (zinc transporter), member 4 1.34 0.04853 −0.34 1417398_at Rras2 Related RAS viral (r-ras) oncogene homolog 2 1.34 0.040085 −0.02 1427203_at Myo15b Myosin XVB 1.33 0.020944 0.92 1428331_at 2210016F16Rik RIKEN cDNA 2210016F16 gene 1.32 0.047659 −0.30 1427128_at Ptpn23 Protein tyrosine phosphatase, non-receptor type 23 1.31 0.042694 −0.13 1420426_at Myo7b Myosin VIIb 1.30 0.036022 0.13 1452304_a_at Arhgef5 Rho guanine nucleotide exchange factor (GEF) 5 1.30 0.047797 −0.31 1434303_at Raph1 Ras association (RalGDS/AF-6) and pleckstrin homology domains 1 1.29 0.024887 0.69 1433885_at AI788777 Expressed sequence AI788777 1.28 0.018321 1.10 1415765_at Hnrpul2 Heterogeneous nuclear ribonucleoprotein U-like 2 1.28 0.009181 2.00 1448110_at Sema4a Serna domain, immunoglobulin domain (Ig), transmembrane domain 1.27 0.00151 4.40 (TM) and short cytoplasmic domain, (semaphorin) 4A 1423960_at Mboat5 Membrane bound O-acyltransferase domain containing 5 1.27 0.043727 −0.18 1415676_a_at Psmb5 Proteasome (prosome, macropain) subunit, beta type 5 1.27 0.040399 −0.04 1434345_at Clrn3 Clarin 3 1.27 0.027133 0.59 1426014_a_at Mucdhl Mucin and cadherin like 1.27 0.036152 0.11 1420503_at Slc6a14 Solute carrier family 6 (neurotransmitter transporter), member 14 1.26 0.001582 4.31 1418817_at Chmp1b Chromatin modifying protein 1B 1.25 0.004961 2.78 1423686_a_at Prr13 Proline rich 13 1.25 0.026919 0.60 1420826_at Letm1 Leucine zipper-EF-hand containing transmembrane protein 1 1.24 0.036022 0.13 1448618_at Mvp Major vault protein 1.24 0.031006 0.39 1417178_at Gipc2 GIPC PDZ domain containing family, member 2 1.24 0.014863 1.38 1416627_at Spint1 Serine protease inhibitor, Kunitz type 1 1.23 0.048555 −0.36 1428163_at Sar1b SARI gene homolog B (S. cerevisiae) 1.22 0.036022 0.13 1416193_at Car1 Carbonic anhydrase 1 1.21 0.009728 1.87 1444884_at Ppt1 Palmitoyl-protein thioesterase 1 1.18 0.032755 0.31 1448279_at Arpc3 Actin related protein ⅔ complex, subunit 3 1.14 0.049367 −0.38 1417282_at Mmp23 Matrix metallopeptidase 23 −1.14 0.024366 0.72 1429615_at Zfp91 Zinc finger protein 91 −1.22 0.038424 0.04 1453577_at 2610018I03Rik RIKEN cDNA 2610018103 gene −1.22 0.04853 −0.35 1417999_at Itm2b Integral membrane protein 2B −1.22 0.020944 0.91 1454994_at Klhl20 Kelch-like 20 (Drosophila) −1.24 0.040433 −0.05 1435563_at Mrps5 Mitochondrial ribosomal protein S5 −1.25 0.022222 0.84 1445561_at NA NA −1.27 0.04853 −0.34 1436854_at Trpc2 Transient receptor potential cation channel, subfamily C, member 2 −1.27 0.002008 3.97 1416452_at Oat Ornithine aminotransferase −1.27 0.009757 1.86 1415961_at Itm2c Integral membrane protein 2C −1.28 0.007369 2.28 1448933_at Pcdhb17 Protocadherin beta 17 −1.28 0.048555 −0.35 1440391_at Gcn1l1 GCN1 general control of amino-acid synthesis 1-like 1 (yeast) −1.29 0.030585 0.42 1450788_at Saa1 Serum amyloid A 1 −1.31 0.001623 4.23 1444451_at Pappa2 Pappalysin 2 −1.31 0.038548 0.03 1457029_at C030010B13Rik RIKEN cDNA C030010B13 gene −1.31 0.023793 0.74 1417088_at Zfp346 Zinc finger protein 346 −1.33 0.039077 0.01 1436220_at Zfp287 Zinc finger protein 287 −1.33 0.022441 0.82 1445824_at Zfp458 Zinc finger protein 458 −1.37 0.044011 −0.18 1420191_s_at D16Bwg1494e DNA segment, Chr 16, Brigham & Women's Genetics 1494 expressed −1.37 0.035165 0.19 1415871_at Tgfbi Transforming growth factor, beta induced −1.38 0.039653 0.00 1442731_at 9030416H16Rik RIKEN cDNA 9030416H16 gene −1.41 0.012107 1.59 1424889_at Nupl2 Nucleoporin like 2 −1.42 0.001582 4.31 1416178_a_at Plekhb1 Pleckstrin homology domain containing, family B (evectins) member 1 −1.44 0.047797 −0.32 1447946_at Adam23 A disintegrin and metallopeptidase domain 23 −1.44 0.017961 1.13 NuGO_emt080869_at NA NA −1.45 0.032755 0.31 1452050_at Camk1d Calcium/calmodulin-dependent protein kinase ID −1.45 0.006002 2.56 1442447_at Znrf3 Zinc and ring finger 3 −1.45 9.00E−06 10.24 1416865_at Fgd1 FYVE, RhoGEF and PH domain containing 1 −1.46 0.049235 −0.37 1442197_at AI480624 Expressed sequence AI480624 −1.47 0.033108 0.27 1427020_at Scara3 Scavenger receptor class A, member 3 −1.47 0.029906 0.45 1434961_at Asb1 Ankyrin repeat and SOCS box-containing protein 1 −1.48 0.0093 1.97 1431873_a_at Tube1 Epsilon-tubulin 1 −1.48 0.033108 0.26 1424367_a_at Homer2 Homer homolog 2 (Drosophila) −1.49 0.00269 3.56 1441662_at Cyp4x1 Cytochrome P450, family 4, subfamily x, polypeptide 1 −1.50 0.028455 0.51 1429086_at Grhl2 Grainyhead-like 2 (Drosophila) −1.51 0.04298 −0.15 1439078_at Klhl4 Kelch-like 4 (Drosophila) −1.52 0.020679 0.96 1451194_at Aldob Aldolase 2, B isoform −1.54 0.002438 3.70 1449913_at Zfp2 Zinc finger protein 2 −1.55 0.033108 0.29 1431820_at 4632404H12Rik RIKEN cDNA 4632404H12 gene −1.56 0.036071 0.12 1437900_at 4930523C07Rik RIKEN cDNA 4930523C07 gene −1.56 0.044391 −0.20 1449462_at 3110049J23Rik RIKEN cDNA 3110049J23 gene −1.57 0.041709 −0.09 1457373_at Cdh19 Cadherin 19, type 2 −1.57 0.032755 0.31 1423072_at 6720475J19Rik RIKEN cDNA 6720475J19 gene −1.58 0.006244 2.51 1422542_at Gpr34 G protein-coupled receptor 34 −1.58 0.040399 −0.04 1448475_at Olfml3 Olfactomedin-like 3 −1.58 0.032964 0.30 1417676_a_at Ptpro Protein tyrosine phosphatase, receptor type, O −1.59 0.001623 4.24 1456763_at AA536749 Expressed sequence AA536749 −1.59 0.017774 1.15 1417732_at Anxa8 Annexin A8 −1.59 0.027267 0.57 1425510_at Mark1 MAP/microtubule affinity-regulating kinase 1 −1.60 0.004814 2.85 1417234_at Mmp11 Matrix metallopeptidase 11 −1.61 0.036152 0.11 1416194_at Cyp4b1 Cytochrome P450, family 4, subfamily b, polypeptide 1 −1.62 0.002404 3.74 1429679_at Fbxl13 F-box and leucine-rich repeat protein 13 −1.64 0.010507 1.76 1428260_at Spg3a Spastic paraplegia 3 A homolog (human) −1.68 0.007369 2.28 1426413_at Neurod1 Neurogenic differentiation 1 −1.68 0.009718 1.88 1455500_at Rnf213 Ring finger protein 213 −1.68 0.017961 1.13 1456532_at Pdgfd Platelet-derived growth factor, D polypeptide −1.70 0.008375 2.11 1419754_at Myo5a Myosin Va −1.71 0.020595 0.97 1460147_at NA NA −1.71 0.037207 0.08 1440014_at Pacs1 Phosphofurin acidic cluster sorting protein 1 −1.72 7.34E−05 8.05 1451342_at Spon1 Spondin 1, (f-spondin) extracellular matrix protein −1.73 0.045023 −0.23 1438530_at Tfpi Tissue factor pathway inhibitor −1.76 0.001582 4.29 1449563_at Cntn1 Contactin 1 −1.77 0.029208 0.48 1435829_at B930008K04Rik RIKEN cDNA B930008K04 gene −1.78 0.004961 2.78 NuGO_emt010210_at Cacna2d2 Calcium channel, voltage-dependent, alpha 2/delta subunit 2 −1.80 0.035702 0.17 1455633_at Zfp647 Zinc finger protein 647 −1.80 0.041245 −0.08 1420416_at Sema3a Serna domain, immunoglobulin domain (Ig), short basic domain, −1.81 0.000506 5.78 secreted, (semaphorin) 3A 1417644_at Sspn Sarcospan −1.83 0.003984 3.08 1419687_at D930010J01Rik RIKEN cDNA D930010J01 gene −1.83 0.045963 −0.25 1439618_at Pde10a Phosphodiesterase 10A −1.83 0.017774 1.16 1440430_at Elp4 Elongation protein 4 homolog (S. cerevisiae) −1.84 0.023065 0.79 1425069_at BC018285 cDNA sequence BC018285 −1.84 0.042264 −0.11 1419376_at 1110018M03Rik RIKEN cDNA 1110018M03 gene −1.85 0.009718 1.88 1434194_at Mtap2 Microtubule-associated protein 2 −1.85 0.007048 2.36 1459707_at Pacs1 Phosphofurin acidic cluster sorting protein 1 −1.86 0.004814 2.86 1434475_at Ppig Peptidyl-prolyl isomerase G (cyclophilin G) −1.86 0.045576 −0.24 1449158_at Kcnk2 Potassium channel, subfamily K, member 2 −1.87 0.004961 2.77 1460606_at Hsd17b13 Hydroxysteroid (17-beta) dehydrogenase 13 −1.88 0.003153 3.38 1436087_at Dpp10 Dipeptidylpeptidase 10 −1.89 0.043727 −0.17 NuGO_emt029633_at Npy2r Neuropeptide Y receptor Y2 −1.90 0.000199 6.88 1418606_at Hoxd10 Homeo box D10 −1.91 0.007866 2.18 1417411_at Nap1l5 Nucleosome assembly protein 1-like 5 −1.91 0.047023 −0.29 NuGO_emt034831_at Nr2e3 Nuclear receptor subfamily 2, group E, member 3 −1.91 0.040798 −0.06 1434740_at Scarf2 Scavenger receptor class F, member 2 −1.91 0.046195 −0.26 1420858_at Pkia Protein kinase inhibitor, alpha −1.92 0.003616 3.21 1457072_at Bcl11a B-cell CLL/lymphoma 11A (zinc finger protein) −1.93 0.04853 −0.35 1428347_at Cyfip2 Cytoplasmic FMR1 interacting protein 2 −1.93 0.000484 5.87 1448823_at Cxcl12 Chemokine (C-X-C motif) ligand 12 −1.95 0.007369 2.28 1436051_at Myo5a Myosin Va −1.95 0.000596 5.61 1425065_at Oas2 2′-5′ oligoadenylate synthetase 2 −1.96 0.032484 0.34 1454876_at Rab23 RAB23, member RAS oncogene family −1.97 0.029208 0.48 NuGO_emt022150_at Cartpt CART prepropeptide −1.98 0.008035 2.16 1423396_at Agt Angiotensinogen (serpin peptidase inhibitor, clade A, member 8) −1.98 0.017774 1.15 1418213_at Krt23 Keratin 23 −1.99 0.031284 0.38 1444670_at Smyd3 SET and MYND domain containing 3 −2.02 0.022766 0.80 1453251_at Dhx30 DEAH (Asp-Glu-Ala-His) box polypeptide 30 −2.03 0.027622 0.56 1440925_at Rhoq Ras homolog gene family, member Q −2.05 0.031006 0.40 1422640_at Pcdhb9 Protocadherin beta 9 −2.07 0.015304 1.34 1450708_at Scg2 Secretogranin II −2.09 0.010099 1.81 1435673_at Hoxd3 Homeo box D3 −2.09 0.029426 0.47 1416710_at Tmem35 Transmembrane protein 35 −2.10 0.007507 2.24 1423150_at Scg5 Secretogranin V −2.11 0.002438 3.69 1418392_a_at Gbp3 Guanylate nucleotide binding protein 3 −2.11 0.020383 0.99 1436566_at Rab40b Rab40b, member RAS oncogene family −2.12 0.003512 3.25 1441231_at EG665123 Predicted gene, EG665123 −2.14 0.035789 0.15 1419349_a_at Cyp2d9 Cytochrome P450, family 2, subfamily d, polypeptide 9 −2.14 0.003512 3.25 1445481_at AI317158 Expressed sequence AI317158 −2.18 0.033108 0.26 1443698_at Fbxo39 F-box protein 39 −2.19 0.009359 1.95 1424900_at Slc29a4 Solute carrier family 29 (nucleoside transporters), member 4 −2.22 0.001105 4.77 1419185_a_at Mlxipl MLX interacting protein-like −2.23 0.000867 5.09 1435504_at Clip4 CAP-GLY domain containing linker protein family, member 4 −2.24 0.006244 2.51 1438868_at Phf11 PHD finger protein 11 −2.24 0.000857 5.12 1422860_at Nts Neurotensin −2.28 1.04E−09 19.02 1451860_a_at Trim30 Tripartite motif protein 30 −2.28 0.038792 0.03 1434788_at D930050A07Rik RIKEN cDNA D930050A07 gene −2.33 0.009359 1.95 1450684_at Etv1 Ets variant gene 1 −2.38 0.000606 5.57 1433536_at Lrp11 Low density lipoprotein receptor-related protein 11 −2.39 0.000793 5.21 NuGO_emt060551_at 9030421J09Rik RIKEN cDNA 9030421J09 gene −2.44 0.044497 −0.20 1428758_at Tmem86a Transmembrane protein 86A −2.45 0.004961 2.76 1445881_at NA NA −2.54 0.031006 0.39 1451426_at D11Lgp2e DNA segment, Chr 11, Lothar Hennighausen 2, expressed −2.55 0.0093 1.98 1416639_at Slc2a5 Solute carrier family 2 (facilitated glucose transporter), member 5 −2.67 0.006738 2.43 1429313_at Ror1 Receptor tyrosine kinase-like orphan receptor 1 −2.70 0.001269 4.59 1433184_at 6720477C19Rik RIKEN cDNA 6720477C19 gene −2.72 0.017774 1.16 1419136_at Akr1c18 Aldo-keto reductase family 1, member C18 −2.77 0.0113 1.66 1418113_at Cyp2d10 Cytochrome P450, family 2, subfamily d, polypeptide 10 −2.79 0.000483 5.90 1417988_at Resp18 Regulated endocrine-specific protein 18 −2.83 0.003512 3.26 1453196_a_at Oasl2 2′-5′ oligoadenylate synthetase-like 2 −2.84 0.011794 1.62 1423555_a_at Ifi44 Interferon-induced protein 44 −2.86 0.042694 −0.13 1449939_s_at Dlk1 Delta-like 1 homolog (Drosophila) −2.99 5.20E−10 19.73 NuGO_emt091063_at NA NA −3.08 0.000637 5.49 1436998_at Ankrd43 Ankyrin repeat domain 43 −3.13 0.001056 4.85 1418293_at Ifit2 Interferon-induced protein with tetratricopeptide repeats 2 −3.14 0.000637 5.44 NuGO_emt044299_at Sstr1 Somatostatin receptor 1 −3.16 2.31E−08 16.00 1421492_at Ptgds2 Prostaglandin D2 synthase 2, hematopoietic −3.18 7.03E−05 8.13 1449025_at Ifit3 Interferon-induced protein with tetratricopeptide repeats 3 −3.34 0.007674 2.21 1455528_at NA NA −3.47 0.002046 3.94 1429273_at Bmper BMP-binding endothelial regulator −3.55 0.000199 6.93 1425952_a_at Gcg Glucagon −3.68 3.98E−09 17.68 1448628_at Scg3 Secretogranin III −3.77 1.61E−08 16.39 1448201_at Sfrp2 Secreted frizzled-related protein 2 −4.18 0.000257 6.62 1418191_at Usp18 Ubiquitin specific peptidase 18 −4.45 0.046848 −0.28 1449493_at Insl5 Insulin-like 5 −9.54 5.98E−16 30.51 1419473_a_at Cck Cholecystokinin −11.97 1.17E−11 23.32

TABLE-US-00027 Table S4C. Transcripts differentially expressed in the ileum at 14d between R. hominis inoculated animals and germfree animals. ID Symbol Name FC P-value B 1427343_at Rasd2 RASD family, member 2 4.21 0.008352 3.02 1420673_a_at Acox2 Acyl-Coenzyme A oxidase 2, branched chain 3.37 0.023445 1.29 1418174_at Dbp D site albumin promoter binding protein 3.26 0.04708 0.16 1434116_at Cbx2 Chromobox homolog 2 (Drosophila Pc class) 3.15 0.01298 2.21 1456284_at Tmem171 Transmembrane protein 171 2.94 0.011378 2.45 1460713_at BC048355 cDNA sequence BC048355 2.61 0.035037 0.67 1438689_at 4632433K11Rik RIKEN cDNA 4632433K11 gene 2.41 0.04048 0.41 1460187_at Sfrp1 Secreted frizzled-related sequence protein 1 2.37 0.021033 1.51 1420645_at Pcgf2 Polycomb group ring finger 2 2.31 0.003987 4.19 1455547_at Zc3h7b Zinc finger CCCH type containing 7B 2.16 0.008352 2.98 1416258_at Tk1 Thymidine kinase 1 2.12 0.017451 1.78 1449845_a_at Ephb4 Eph receptor B4 2.12 0.033002 0.77 1455120_at Hpdl 4-hydroxyphenylpyruvate dioxygenase-like 2.07 0.023445 1.30 1417399_at Gas6 Growth arrest specific 6 2.06 0.000167 8.81 1452862_at Rreb1 Ras responsive element binding protein 1 2.05 0.03901 0.47 1455246_at NA NA 2.02 0.032868 0.78 1434322_at Micall2 MICAL-like 2 1.99 0.009875 2.69 1428207_at Bcl7a B-cell CLL/lymphoma 7A 1.99 0.04708 0.11 1420845_at Mrps2 Mitochondrial ribosomal protein S2 1.97 0.042267 0.36 1444254_at NA NA 1.96 0.025132 1.19 1448656_at Cacnb3 Calcium channel, voltage-dependent, beta 3 subunit 1.96 0.032019 0.86 1434908_at AI480556 Expressed sequence AI480556 1.95 0.029591 0.99 1424376_at Cdc42ep1 CDC42 effector protein (Rho GTPase binding) 1 1.89 0.01298 2.20 1430274_a_at Stard3nl STARD3 N-terminal like 1.88 0.008596 2.92 1416513_at Lamb2 Laminin, beta 2 1.87 0.016398 1.89 1416536_at Mum1 Melanoma associated antigen (mutated) 1 1.86 0.025132 1.17 NuGO_emt084041_s_at Defcr20 Defensin related cryptdin 20 1.84 0.020502 1.55 1418320_at Prss8 Protease, serine, 8 (prostasin) 1.83 0.021033 1.49 1455163_at Guf1 GUF1 GTPase homolog (S. cerevisiae) 1.80 0.02461 1.22 1436665_a_at Ltbp4 Latent transforming growth factor beta binding protein 4 1.80 0.036581 0.57 1420643_at Lfng Lunatic fringe gene homolog (Drosophila) 1.79 0.003248 4.57 1428695_at 9130227C08Rik RIKEN cDNA 9130227C08Rik gene 1.79 0.036167 0.59 1453018_at Nvl Nuclear VCP-like 1.77 0.035037 0.65 1419101_at Sin3a Transcriptional regulator, SIN3A (yeast) 1.76 0.030882 0.91 1424459_at Aytl2 Acyltransferase like 2 1.74 0.039921 0.43 1415935_at Smoc2 SPARC related modular calcium binding 2 1.73 0.04615 0.19 1424618_at Hpd 4-hydroxyphenylpyruvic acid dioxygenase 1.73 0.03901 0.47 1426297_at Tcfe2a Transcription factor E2a 1.73 0.002215 5.11 1425391_a_at Osbpl5 Oxysterol binding protein-like 5 1.73 0.04615 0.19 1455719_at Tubb5 Tubulin, beta 5 1.73 0.032477 0.82 1451912_a_at Fgfrl1 Fibroblast growth factor receptor-like 1 1.73 0.02321 1.33 1429582_at Btbd14a BTB (POZ) domain containing 14A 1.72 0.003987 4.21 1454777_at Slco2b1 Solute carrier organic anion transporter family, member 2b1 1.70 0.01298 2.22 1424101_at Hnrpl Heterogeneous nuclear ribonucleoprotein L 1.69 0.044481 0.25 1448691_at Ubqln4 Ubiquilin 4 1.65 0.016054 1.92 1417604_at Camk1 Calcium/calmodulin-dependent protein kinase I 1.63 0.033233 0.74 1442757_at Lrch1 Leucine-rich repeats and calponin homology (CH) domain 1.63 0.007505 3.30 containing 1 1460675_at Igsf8 Immunoglobulin superfamily, member 8 1.62 0.04708 0.13 1418671_at Capn5 Calpain 5 1.58 0.04708 0.15 1426897_at Rcc2 Regulator of chromosome condensation 2 1.57 0.035037 0.65 1417594_at Gkap1 G kinase anchoring protein 1 1.52 0.019831 1.60 1433539_at Commd3 COMM domain containing 3 1.51 0.009875 2.72 1435469_at Qscn6l1 Quiescin Q6-like 1 1.51 0.041412 0.38 1448561_at Ncf2 Neutrophil cytosolic factor 2 1.51 0.044087 0.30 1427022_at Ddx42 DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 1.50 0.01872 1.67 1416030_a_at Mcm7 Minichromosome maintenance deficient 7 (S. cerevisiae) 1.49 0.02321 1.34 1450023_at Gtpbp1 GTP binding protein 1 1.48 0.044113 0.27 1417879_at Nenf Neuron derived neurotrophic factor 1.48 0.03901 0.46 1424640_at Arl8a ADP-ribosylation factor-like 8A 1.47 0.044113 0.28 1418982_at Cebpa CCAAT/enhancer binding protein (C/EBP), alpha 1.47 0.036167 0.60 1428382_at Smarcc2 SWI/SNF related, matrix associated, actin dependent regulator 1.47 0.044113 0.28 of chromatin, subfamily c, member 2 1434134_at Wdr42a WD repeat domain 42A 1.45 0.009875 2.74 1450519_a_at Prkaca Protein kinase, cAMP dependent, catalytic, alpha 1.44 0.008352 2.99 1451306_at Cdca7l Cell division cycle associated 7 like 1.44 0.035037 0.65 1426724_at Cnn3 Calponin 3, acidic 1.44 0.033105 0.76 1424644_at Tbcc Tubulin-specific chaperone c 1.42 0.032128 0.85 1417266_at Ccl6 Chemokine (C-C motif) ligand 6 1.42 0.021206 1.47 1415975_at Carhsp1 Calcium regulated heat stable protein 1 1.38 0.014132 2.10 1448277_at Pold2 Polymerase (DNA directed), delta 2, regulatory subunit 1.38 0.044481 0.24 1433736_at Hcfc1 Host cell factor C1 1.35 0.035162 0.64 1435149_at Plcg1 Phospholipase C, gamma 1 1.35 0.036167 0.59 1417500_a_at Tgm2 Transglutaminase 2, C polypeptide 1.33 0.022457 1.39 1428125_at 4921506J03Rik RIKEN cDNA 4921506J03 gene 1.32 0.030752 0.92 1452100_at Dullard Dullard homolog (Xenopus laevis) 1.32 0.030391 0.94 1448148_at Grn Granulin 1.30 0.011783 2.33 1451984_at Hnrpul1 Heterogeneous nuclear ribonucleoprotein U-like 1 1.30 0.016884 1.85 1426401_at Ppp3ca Protein phosphatase 3, catalytic subunit, alpha isoform 1.29 0.009875 2.72 1428380_at 0610007C21Rik RIKEN cDNA 0610007C21 gene 1.26 0.043354 0.32 1418364_a_at Ftl1 Ferritin light chain 1 1.24 0.01702 1.82 1456854_at Neurl Neuralized-like homolog (Drosophila) −1.18 0.031207 0.89 1448853_at Synj2bp Synaptojanin 2 binding protein −1.19 0.04708 0.15 1416281_at Wdr45l Wdr45 like −1.22 0.016971 1.84 1418843_at Slc30a4 Solute carrier family 30 (zinc transporter), member 4 −1.30 0.037239 0.54 1459557_at Zbtb16 Zinc finger and BTB domain containing 16 −1.31 0.001423 5.62 1418116_at Ifrg15 Interferon alpha responsive gene −1.32 0.038411 0.50 1448762_at Rad17 RAD 17 homolog (S. pombe) −1.32 0.044087 0.30 1435461_at Magi3 Membrane associated guanylate kinase, WW and PDZ domain −1.33 0.044113 0.26 containing 3 1434835_at Wapal Wings apart-like homolog (Drosophila) −1.33 0.046851 0.17 1444328_at NA NA −1.34 0.010408 2.57 NuGO_emt073151_at Nlrp9b NLR family, pyrin domain containing 9B −1.34 0.045959 0.20 1427269_at Sfrs11 Splicing factor, arginine/serine-rich 11 −1.35 0.02461 1.22 1436157_at Ccar1 Cell division cycle and apoptosis regulator 1 −1.36 0.021206 1.46 NuGO_emt081039_at Eif4e1b Eukaryotic translation initiation factor 4E family member 1B −1.38 0.037239 0.54 1422217_a_at Cyp1a1 Cytochrome P450, family 1, subfamily a, polypeptide 1 −1.38 0.005253 3.71 1434654_at Cog3 Component of oligomeric golgi complex 3 −1.38 0.03901 0.46 1421680_at NA NA −1.39 0.044113 0.28 1424296_at Gclc Glutamate-cysteine ligase, catalytic subunit −1.41 0.023137 1.36 1440722_at D19Ertd386e DNA segment, Chr 19, ERATO Doi 386, expressed −1.41 0.008352 3.15 1429849_at 4632411B12Rik RIKEN cDNA 4632411B12 gene −1.44 0.015927 1.94 1451407_at Jam4 Junction adhesion molecule 4 −1.44 0.015521 1.99 1424324_at Esco1 Establishment of cohesion 1 homolog 1 (S. cerevisiae) −1.47 0.010277 2.60 1441403_at 6430501K19Rik RIKEN cDNA 6430501K19 gene −1.47 0.019952 1.59 1453160_at Thrap1 Thyroid hormone receptor associated protein 1 −1.48 0.034193 0.71 1432962_at 2610024D14Rik RIKEN cDNA 2610024D14 gene −1.49 0.018436 1.70 1456896_at 6720462K09Rik RIKEN cDNA 6720462K09 gene −1.50 0.011783 2.34 1444705_at App Amyloid beta (A4) precursor protein −1.50 0.032477 0.80 1426886_at Cln5 Ceroid-lipofuscinosis, neuronal 5 −1.52 0.01702 1.81 1459059_at 2010308F09Rik RIKEN cDNA 2010308F09 gene −1.53 0.008352 2.97 1436616_at R74740 Expressed sequence R74740 −1.55 0.011378 2.44 1453269_at Unc5b Unc-5 homolog B (C. elegans) −1.55 0.018436 1.70 1424536_at Oas1e 2′-5′ oligoadenylate synthetase 1E −1.55 0.008352 3.08 1444565_at NA NA −1.56 0.005253 3.70 1448049_at Jmjd1c Jumonji domain containing 1C −1.58 0.02321 1.33 1441546_at Mpp6 Membrane protein, palmitoylated 6 (MAGUK p55 subfamily −1.58 0.009875 2.70 member 6) 1442605_at Bach2 BTB and CNC homology 2 −1.59 0.032477 0.80 1451415_at 1810011O10Rik RIKEN cDNA 1810011O10 gene −1.66 0.023445 1.29 1436637_at Eif4h Eukaryotic translation initiation factor 4H −1.66 0.011571 2.40 1453457_at Sri Sorcin −1.67 0.024152 1.25 1429680_at Tra2a Transformer 2 alpha homolog (Drosophila) −1.68 0.033105 0.75 1429624_at Sltm SAFB-like, transcription modulator −1.68 0.036906 0.56 1429870_at Tnik TRAF2 and NCK interacting kinase −1.72 0.001356 5.94 1444065_at Cyb5d2 Cytochrome b5 domain containing 2 −1.72 0.000237 8.03 1424208_at Ptger4 Prostaglandin E receptor 4 (subtype EP4) −1.74 0.029592 0.98 1452837_at Lpin2 Lipin 2 −1.74 0.011783 2.33 1448185_at Herpud1 Homocysteine-inducible, endoplasmic reticulum stress- −1.75 0.002895 4.81 inducible, ubiquitin-like domain member 1 1432719_at 4833412K13Rik RIKEN cDNA 4833412K13 gene −1.76 0.04708 0.13 1437868_at BC023892 cDNA sequence BC023892 −1.76 0.044113 0.28 1433101_at 9030419F21Rik RIKEN cDNA 9030419F21 gene −1.77 0.008596 2.90 1451621_at 5830417C01Rik RIKEN cDNA 5830417C01 gene −1.77 0.00495 3.81 1432423_a_at C530008M17Rik RIKEN cDNA C530008M17 gene −1.78 0.01164 2.38 1429399_at Rnf125 Ring finger protein 125 −1.84 0.033002 0.77 1453264_at Marveld3 MARVEL (membrane-associating) domain containing 3 −1.86 4.82E−05 10.38 1454343_at Ppapdc1 Phosphatidic acid phosphatase type 2 domain containing 1 −1.88 0.003658 4.42 1435571_at A530065I17Rik RIKEN cDNA A530065I17 gene −1.90 0.015795 1.96 1443164_at NA NA −1.91 0.010163 2.63 1437776_at Tmcc1 Transmembrane and coiled coil domains 1 −1.91 0.028192 1.04 1442111_at D430033H22Rik RIKEN cDNA D430033H22 gene −1.91 0.007072 3.40 1424451_at Acaa1b Acetyl-Coenzyme A acyltransferase 1B −1.92 0.035037 0.67 1459879_at 4921513D23Rik RIKEN cDNA 4921513D23 gene −1.92 0.008352 2.99 1428776_at Slc10a6 Solute carrier family 10 (sodium/bile acid cotransporter family), −1.92 0.011378 2.45 member 6 1458079_at Usp40 Ubiquitin specific peptidase 40 −1.93 0.004696 3.98 1442897_at 2610024E20Rik RIKEN cDNA 2610024E20 gene −1.95 0.00402 4.15 1455744_at Tmem181 Transmembrane protein 181 −1.97 0.037843 0.52 1449385_at Hsd17b6 Hydroxysteroid (17-beta) dehydrogenase 6 −1.98 0.025132 1.18 1443068_at D130084N16Rik RIKEN cDNA D130084N16 gene −1.98 0.04708 0.11 1419582_at Cyp2c55 Cytochrome P450, family 2, subfamily c, polypeptide 55 −1.99 0.042267 0.35 1457801_at 9930024M15Rik RIKEN cDNA 9930024M15 gene −2.01 0.04708 0.13 1438331_at Ypel2 Yippee-like 2 (Drosophila) −2.02 0.037843 0.51 1428833_at 4930406D14Rik RIKEN cDNA 4930406D14 gene −2.04 0.015418 2.01 1419388_at Tm4sf20 Transmembrane 4 L six family member 20 −2.05 0.010163 2.65 1455510_at Spop Speckle-type POZ protein −2.08 0.023445 1.29 1444178_at ENSMUSG00000052976 Predicted gene, ENSMUSG00000052976 −2.09 0.029592 0.97 1443159_at Txnrd1 Thioredoxin reductase 1 −2.10 0.04708 0.11 1457161_at 9530029O12Rik RIKEN cDNA 9530029012 gene −2.11 0.019032 1.65 1459887_at NA NA −2.11 0.003987 4.29 1459005_at NA NA −2.13 0.007384 3.34 1439283_at NA NA −2.18 0.007823 3.24 1438338_at Mdh1 Malate dehydrogenase 1, NAD (soluble) −2.21 0.001446 5.54 1458452_at NA NA −2.21 0.010277 2.59 1442256_at Prkcd Protein kinase C, delta −2.21 0.026633 1.11 1443969_at Irs2 Insulin receptor substrate 2 −2.22 0.003987 4.22 1452462 a_at Banp Btg3 associated nuclear protein −2.30 0.021033 1.52 1454558_at 5430416B10Rik RIKEN cDNA 5430416B10 gene −2.32 1.71E−07 15.68 1430393_at C030048B08Rik RIKEN cDNA C030048B08 gene −2.32 0.001388 5.78 1446929_at Bach2 BTB and CNC homology 2 −2.32 0.027369 1.07 NuGO_emt067737_at 9130230L23Rik RIKEN cDNA 9130230L23 gene −2.34 0.04708 0.15 1441138_at Foxn2 Forkhead box N2 −2.36 0.001356 6.01 1416041_at Sgk Serum/glucocorticoid regulated kinase −2.40 0.04048 0.41 145415 8_at Mpp7 Membrane protein, palmitoylated 7 (MAGUK p55 subfamily −2.40 0.011571 2.40 member 7) 1459253_at Arrdc3 Arrestin domain containing 3 −2.46 0.044113 0.27 1444376_at Sesn1 Sestrin 1 −2.48 0.036167 0.59 1430362_at 5730409N24Rik RIKEN cDNA 5730409N24 gene −2.49 0.032477 0.83 1442069_at D5Wsu178e DNA segment, Chr 5, Wayne State University 178, expressed −2.50 0.032477 0.80 1433203_at 6030400A10Rik RIKEN cDNA 6030400A10 gene −2.56 0.000747 6.76 1456706_at 1700109H08Rik RIKEN cDNA 1700109H08 gene −2.60 0.004825 3.89 1441561_at Fbxl3 F-box and leucine-rich repeat protein 3 −2.60 0.034193 0.70 1437884_at Arl5b ADP-ribosylation factor-like 5B −2.65 0.022457 1.40 1445843_at Chd2 Chromodomain helicase DNA binding protein 2 −2.66 0.044481 0.24 1428306_at Ddit4 DNA-damage-inducible transcript 4 −2.66 0.008352 3.09 1421009_at Rsad2 Radical S-adenosyl methionine domain containing 2 −2.69 0.04708 0.14 1440227_at BF642829 Expressed sequence BF642829 −2.69 0.026633 1.11 1453595_at Bcl6 B-cell leukemia/lymphoma 6 −2.70 0.004825 3.89 1444775_at 9930033D15Rik RIKEN cDNA 9930033D15 gene −2.71 0.003248 4.61 1439972_at Etnk1 Ethanolamine kinase 1 −2.74 0.032477 0.83 1440536_at Slc22a5 Solute carrier family 22 (organic cation transporter), member 5 −2.90 0.021033 1.49 1438660_at Gcnt2 Glucosaminyl (N-acetyl) transferase 2,1-branching enzyme −2.95 0.018436 1.70 1437759_at Pfkp Phosphofructokinase, platelet −2.97 0.008352 3.11 NuGO_emt050020_at Amica1 Adhesion molecule, interacts with CXADR antigen 1 −2.97 0.000981 6.41 1446950_at Tox Thymocyte selection-associated HMGbox gene −3.00 0.008352 2.98 1447141_at AW107722 Expressed sequence AW107722 −3.14 0.013251 2.17 1459219_at Rapgef2 Rap guanine nucleotide exchange factor (GEF) 2 −3.21 0.000747 6.75 1449496_at 2010109I03Rik RIKEN cDNA 2010109103 gene −3.22 0.000167 8.69 1458296_at NA NA −3.23 0.001388 5.70 1440749_at NA NA −3.38 0.001388 5.76 1440892_at BC017647 cDNA sequence BC017647 −3.52 0.004881 3.85 1441115_at Rnf125 Ring finger protein 125 −3.90 0.000237 8.14 1421365_at Fst Follistatin −4.33 0.04708 0.12 1446972_at D15Wsu126e DNA segment, Chr 15, Wayne State University 126, expressed −7.09 0.003054 4.72

TABLE-US-00028 Table S4D. Transcripts differentially expressed in the ileum at 28d between R. hominis inoculated animals and germfree animals. ID Symbol Name M P-value B 1458427_at Brip1 BRCA1 interacting protein C- −1.72 0.002194 4.97 terminal helicase 1

Genes involved in innate immunity and gut barrier function were significantly induced by the presence of R. hominis in the ascending colon. The GO-process ‘innate immune response’ (GO:0045087) was up-regulated and included the important TLR-related genes Tlr5, Tlr1 and Vnn1. The up-regulation of Tlr5 was of particular interest, given the corresponding induction of flagellar genes and flagellin protein in R. hominis during gut colonization, and may infer a role for this innate signalling pathway in mediating innate and adaptive immune responses. Other innate immune genes affected in the colon by R. hominis included the antimicrobial peptides Defb37, Pla2 g3, Mucl6 and Itln and the gut barrier function genes Sprr1a, CIdn4, Pmp22, Crb3 and Mag13. Innate immune genes showing up-regulation in the ileum in response to R. hominis included Defcr20, Pcgf2, Ltbp4, Igsf8 and Tcfe2a. Interestingly, herein it is shown negative regulation of the NF-κB pathway (GO:0043124) (FIG. 9A-9C) by R. hominis, which, like B. thetaiotaomicron (Kelly et al. 2004), may contribute to immune homeostasis by down-regulating this inflammatory cascade.

To demonstrate that these responses are specific to R. hominis, the response of germfree animals to another commensal bacterium was investigated. The gene expression responses to colonization with E. coli MG1655 (1(12) were compared to R. hominis after 10-14d and 22-28d post-colonization. Over this time interval, large differences in gene expression were observed in response to R. hominis but not to E. coli, indicating that R. hominis is biologically very active in the gut, in contrast to the minimal impact of E. coli (FIG. 10). The response to E. coli deduced from the gene expression data in the ascending colon seemed to be mainly a B-cell mediated antibody response.

R. hominis Affects T Cell Pathways Mostly in the Colon

The majority of pathways affected at 14d grouped into the categories cell differentiation, cell cycle regulation and tissue remodelling. Importantly, immune response was a major pathway induced at 28d in the ascending colon. The significantly affected pathways in this category were mostly involved in T cell function, including IL-10 signalling and regulation of T cell function by CTLA-4 (Table S5). The genes involved in these pathways showed both up-regulation and down-regulation, so while these pathways were significantly affected by the presence of R. hominis, the precise net functional effects on T cell differentiation required further investigation. To clarify the role of R. hominis in relation to T cell differentiation, conventional mice with R. hominis were treated for 14 days and determined the impact on T cell subsets both in the lamina propria and mesenteric lymph nodes (MLN). Treatment with R. hominis increased the population of CD3⁺CD4⁺CD25⁺FoxP3⁺ T cells in both locations (FIG. 4). An assessment was made of the numbers of double-positive CD3⁺FoxP3⁺ cells in the lamina propria of ascending and descending colon of mono-associated C3H/HeN and C57B16 animals and confirmed a significant increase in regulatory T cells in R. hominis-treated mice (FIG. 5A). The GO-process for ‘actin polymerization’ (GO:0030041) (Arpc3, Capg, Cdc42ep5 and Rhoc) was up-regulated at 28d in the colon in R. hominis colonized mice (FIG. 9A-C). Actin polymerization at the immune synapse is required for T cell activation and effector function. Overall, this data indicates that R. hominis actively effects the adaptive immune response in the colon by positively influencing T cell regulation.

TABLE-US-00029 Table S5. Immune system response pathway analysis of transcripts differentially expressed in the ascending colon between R. hominis treated mice and germfree mice at 28d. Regulatory processes/lmmune system response pathway P-value Significant* Total** Immune response_IL-10 signaling pathway 0.00125 10 26 Immune response_IL-9 signaling pathway 0.00592 11 36 Immune response_HMGB1/RAGE signaling pathway 0.00832 14 53 Immune response_BCR pathway 0.00992 14 54 Development_GM-CSF signaling 0.01258 13 50 Development_PEDF signaling 0.02618 12 49 Immune response_IL-5 signalling 0.02840 11 44 Immune response_TCR and CD28 co-stimulation in activation 0.03611 10 40

Immune response_Regulation of T cell function by CTLA-4 0.04598 9 36 Immune response_CD40 signaling 0.04796 14 65 Signal transduction_JNK pathway 0.04921 10 42 Differentially expressed genes (P < 0.05) were imported into GeneGo MetaCore analytical software to determine significantly enriched canonical pathways in each group. *The number of genes on each map that are differentially expressed in the specific treatment comparison. **The total number of genes on each map.

indicates data missing or illegible when filed

Related to these results was the induction of the Ly6 gene family in the ascending colon. In particular, the GPI-anchored gene product of Ly6 g6c was up-regulated 25-fold, and the related gene Ly6 g6e was up-regulated two-fold at 28d. Most haematopoietic cells, including neutrophils and plasmacytoid dendritic cells, express one or more members of the Ly6 family. Furthermore, a possible role of Ly6 in T cell activation, differentiation and maturation has been proposed (Mallya, Campbell & Aguado 2006). Immunocytochemistry confirmed increased presence of Ly6G⁺, CD11b⁺ and CD3⁺FoxP3⁺ cells in R. hominis-colonized mice (FIG. 5B-5E).

R. hominis Flagellins Modulate T Cell Differentiation

The influence of bacteria on the differentiation of T cells may reflect the array of TLR ligands displayed. For example, the coupling between TLR5 signalling and CD4⁺ T cell responses has recently been demonstrated for flagellate pathogens (Letran et al. 2011). Interestingly, depending upon the experimental setting, flagellin can prime a range of T cell responses including Th1, Th2, Th17 and Treg responses (Wilson et al. 2012).

The functionality of bacterial flagellins FlaA1 (RH1) and FlaA2 (RH2) was investigated using novel soluble recombinant flagellin proteins, generated against the unique R. hominis flagellin sequences. The ability of RH1 and RH2 were compared and contrasted with various commensal and pathogenic flagellins, generated using identical protocols, to activate signalling responses in intestinal epithelial cell lines and bone marrow derived dendritic cells expanded with either FLT3L or GM-CSF.

Epithelial cells treated with identical concentrations of different bacterial flagellins revealed distinct patterns of gene expression (FIG. 6A). Importantly, no endotoxin contamination was detected in the recombinant protein preparations. Salmonella enteritidis (SE) was more potent than E. coli K12 (EC) or RH1 flagellin. RH1 flagellin also showed a strong response but clustered in a distinct clad along with commensal EC. The responses were shown to be TLR5-dependent using epithelial cells expressing dominant-negative TLR5. In contrast, RH2 was shown to be minimally active; it was generally not pro-inflammatory nor did it activate the conserved gene signature (IL-8, CXCL-1, CXCL-2 and CXCL-10) induced by other recombinant bacterial flagellins. RH1 flagellin protein is more biologically active than RH2 in vitro; although both recombinant proteins were expressed in vivo, RH1 was also significantly up-regulated at the gene expression level in vivo. It was demonstrated that the RH1 flagellin from R. hominis induced different responses in Flt3L and GM-CSF derived dendritic cells relative to commensal E. coli and pathogenic Salmonella enteritidis (FIG. 6E). In particular, RH1 was unique in its ability to activate Flt3L-expanded DCs, with up-regulation of I-A/I-E and CD40 and the production of IL-10 by bone marrow derived DCs from both C3H/HeN and C57Bl/6 mice. The IL-10/IL-12 ratio was particularly elevated in C57Bl/6 DCs (FIG. 6F), which were found to be CD103+ Siglec-H+. Consistent with the observations herein, a number of recent reports have also shown that flagellin can activate CD103+DC populations (Flores-Langarica et al. 2012, Kinnebrew et al. 2012).

To evaluate the functional importance of R. hominis and its flagellins, germ-free TLR5KO and WT mice were mono-colonized. The heatmap showing differentially expressed genes for both TLR5KO and wild-type colonized with R. hominis revealed a very strong effect of TLR5 (FIG. 11). Although T cell pathways were still influenced by R. hominis colonization in TLR5KO mice, the responses were more related to IL4, IL5, IL-6, IL-9 pathways and not IL-10 and CTLA-4 (Table S6). Furthermore, the numbers of double-positive CD3⁺FoxP3⁺ cells in the lamina propria of TLR5KO mice were not increased by R. hominis treatment (FIG. 6G), in contrast to mono-associated C3H/HeN and C57B16 animals (FIG. 5A).

TABLE-US-00030 Table S6. Immune system response pathway analysis of transcripts differentially expressed in the ascending colon between TLR5 KO mice and WT mice, mono-colonized with R. hominis. # Maps pValue Ratio 1 Immune response_IL-9 signaling pathway 0.00001 7 36 2 Immune response_Histamine signaling in dendritic cells 0.00008 7 50 3 Immune response_HMGB1/RAGE signaling pathway 0.00012 7 53 4 Immune response_IL-6 signaling pathway 0.00046 5 31 5 Immune response_Histamine H1 receptor signaling in immune 0.00052 6 48 response 6 Immune response_Oncostatin M signaling via MAPK in mouse cells 0.00082 5 35 7 Immune response_Oncostatin M signaling via MAPK in human cells 0.00107 5 37 8 Signal transduction_JNK pathway 0.00191 5 42 9 Immune response_IL-7 signaling in B lymphocytes 0.00213 5 43 10 Immune response_Signaling pathway mediated by IL-6 and IL-1 0.00362 4 30 11 Development_GM-CSF signaling 0.00415 5 50 12 Immune response_T cell receptor signaling pathway 0.00492 5 52 13 Chemotaxis_Leukocyte chemotaxis 0.00528 6 75 14 Immune response_CCL2 signaling 0.00579 5 54 15 Immune response_CD28 signaling 0.00579 5 54 16 Immune response_Role of DAP12 receptors in NK cells 0.00579 5 54 17 Immune response_Fc epsilon RI pathway 0.00626 5 55 18 Immune response_Role of PKR in stress-induced antiviral cell 0.00728 5 57 response 19 Immune response_HMGB1 release from the cell 0.01114 4 41 20 Immune response_IL-15 signaling 0.01176 5 64 21 Immune response_HTR2A-induced activation of cPLA2 0.01313 4 43 22 Immune response_IL-4 signaling pathway 0.01421 4 44 23 Immune response_IL-5 signalling 0.01421 4 44 24 Immune response_Fc gamma R-mediated phagocytosis in 0.01653 4 46 macrophages 25 Immune response_NF-AT signaling and leukocyte interactions 0.01653 4 46 26 Development_PEDF signaling 0.02043 4 49 27 Immune response_IL-2 activation and signaling pathway 0.02043 4 49 28 Immune response_NFAT in immune response 0.02332 4 51 29 Immune response_IL-3 activation and signaling pathway 0.02803 3 31 30 Immune response_BCR pathway 0.02809 4 54 31 Immune response_TLR signaling pathways 0.02809 4 54 32 Immune response_Immunological synapse formation 0.03727 4 59 33 Immune response_Th17 cell differentiation 0.03836 3 35 34 Immune response_Human NKG2D signaling 0.04722 3 38 Differentially expressed genes (P < 0.05) were imported into GeneGo MetaCore analytical software to determine significantly enriched canonical pathways in each group. *The number of genes on each map that are differentially expressed in the specific treatment comparison. **The total number of genes on each map.

The observation herein that R. hominis influences Tregs in conventional and germ-free mice and not in TLR5KO is consistent with reports of flagelling TLR5 interactions promoting CD4⁺CD25⁺Foxp3⁺ regulatory T cells (Crellin et al. 2005, Hossain et al. 2011). Similarly, the ability of a flagellin-ovalbumin fusion protein to suppress IL-4 production by OVA-T-cell receptor CD4(+) T cells via an IL-10 dependent mechanism has recently been described (Schulke et al. 2011) indicating that flagellin can influence the directional differentiation of T cell subsets. In addition, the impact of the TLR5KO on T cells responses driven by R. hominis infers that RH1 (the signalling flagellin) was crucial in mediating the Treg responses and not RH2 (the non-signaling flagellin). Finally, an additional observation was the enhancement of Type I IFN genes in TLR5KO mice (including Ifi202b, Ifi1203 and Irf4), which suggests that TLR5 signalling may dampen Type I interferon responses.

R. hominis Modulates Innate Immune Response Genes in Both the Ileum and Colon and Attenuates Colitis in DSS-Treated Mice

The DSS mouse model was used to test the therapeutic efficacy of R. hominis, due to the control of inflammatory pathways as well as the positive effects on Treg induction in mono-associated mice. Mice were dosed (˜50 μL, 10⁹ CFU) daily for a period of 14 days, and given DSS (MW 50 kDa, 30 g/1) in their drinking water from day 8 onwards. Gene expression of a panel of pro-inflammatory biomarkers showed that untreated DSS mice had strong elevation of all investigated genes compared to wild-type mice, with gene induction ranging from 4- to 49-fold (FIG. 7A). Pro-inflammatory gene induction was significantly lower in R. hominis-treated compared to untreated mice, indicating strong therapeutic benefits of oral administration of R. hominis. Histological analysis showed the presence of severe inflammation in the ascending colon of untreated DSS, while the colonic mucosa of R. hominis-treated animals was normal, with low-level inflammation, consistent with the reduced inflammatory gene expression (FIGS. 7B and C).

R. hominis Colonization Influences Body Composition and Expression of Satiety Genes

Significant metabolic actions of R. hominis in mono-associated mice were also evident. The GO-processes ‘negative regulation of response to food’ (GO:0032096), ‘negative regulation of appetite’ (GO:0032099), and ‘regulation of catecholamine secretion’ (GO:0050433) were all down-regulated in the ascending colon after colonization with R. hominis (FIGS. 12A-J). This data infers that R. hominis exerts a stimulatory effect on host appetite. The genes involved in these processes were Agt, Cartpt, Cck and Cxcl12, with fold-changes ranging from 2- to 12-fold. Cck, in particular, plays a major role in digestion and satiety as a hunger suppressant. Gcg also showed down-regulation at this gut site.

To establish whether these gene changes had physiological relevance in relation to food intake and body composition, dry carcass weight and composition analyses were performed. The dry carcass weights of R. hominis-associated mice were significantly heavier compared to GF animals, and the differences were most discernible at 14d (FIG. 13A). Further carcass lipid analysis showed that total adiposity was also significantly higher in R. hominis-treated animals at 14d (FIG. 13B). These findings are consistent with recent data revealing the role of Firmicutes in energy harvest through dietary fermentation, but also support the notion that gut bacteria can in fact modulate the brain-gut axis and appetite-regulating hormones.

DISCUSSION

The long-term co-evolution of host-microbe mutualism has likely driven the selection of functionally important bacterial species in the gut, the majority of which are not highly represented in other ecosystems. Currently, there is limited information regarding the contribution of individual members of the microbial community to intestinal functions, particularly in relation to development of the mucosal immune system.

Recent work using a reversible colonization model based on E. coli (HA 107) has demonstrated that live bacteria are required in numbers approaching 10⁸ CFUs per gram of content for the immune-inducing effects on IgA (Hapfelmeier et al. 2010). The specific functions of SFB and Bacteroides fragilis have been investigated in the mouse gut to define their individual contributions to T cell biology and both these bacteria have been shown to be potent inducers of Tregs and Th17 cells (Mazmanian et al. 2005, Gaboriau-Routhiau et al. 2009, Ivanov et al. 2009). The effects of individual members of the cluster XIVa Firmicutes have not been reported previously, although their presence in the ASF and the contribution of a mixed culture of 46 Clostridial strains, which also affects T cell differentiation has been noted (Geuking et al. 2011, Atarashi et al. 2011).

Reported here is the first successful mono-association of the germ-free mouse gut with an anaerobic bacterium, R. hominis, which is a member of the Firmicutes phylum. The extreme oxygen sensitivity of bacteria like Roseburia requires strict anaerobic culture techniques, making it difficult to perform functional characterization. The stable mono-colonization of R. hominis in germfree mice has been established and the complete annotated genomic sequence to uncover its metabolic organization, physiology, and symbiotic properties has been produced. It was found that the transcriptional responses of R. hominis following colonization could be attributed to both the host gut environment and diet. The host-driven effects dominated the response of R. hominis following mono-association. These included gene transfer, membrane transport, chemotaxis and motility subsystems. The strong up-regulation of genes involved in mobilization transfer supports the view that the gut environment is highly conducive to horizontal gene exchange between members of the gut microbiota. Thus, this environment may accelerate the dissemination of genes important for bacterial survival, colonization and function within the gut ecosystem. The role of motility and flagellar apparatus in host colonization is well-elaborated for pathogenic bacteria but much less is known about the role of flagellar proteins in commensal bacteria. In vivo experiments revealed a stimulatory effect of the host intestinal environment on the expression of flagellin genes.

A clear role for R. hominis in promoting gut barrier function and innate immunity in the mouse colon has been established. Tight junctions, gap junctions and adherens junctions operate to limit bacterial translocation to the subepithelial layer (Werth et al. 2010). Both Crohn's disease and ulcerative colitis are characterized by loss of barrier function and tight junction integrity. Interestingly, dysbiosis of the gut microbiota in IBD is associated with a reduction in Firmicutes (Spor, Koren & Ley 2011, Qin et al. 2010). The observation herein that R. hominis actively enhances the expression of barrier genes suggests that their loss in IBD patients may be functionally significant. Activation of tight junction complexes is not just the prerogative of R. hominis; other commensals, such as Bacteroides thetaiotaomicron and Lactobacillus acidophilus, also enhance mucosal barrier function (Hooper et al. 2001, Ukena et al. 2007), inferring probiotic opportunities with these bacteria in human IBD.

The effects of R. hominis on the gut immune system are intriguing. The strongest effects were noted in the ascending colon and genes such as Ly6 g6c were strongly up-regulated, as well as pathways involved in T cell regulation and differentiation and actin polymerization at the immune synapse, which are implicated in T cell activation and effector functions. The most affected T cell pathways included those related to IL-10, ICOS and CTLA-4, which are all involved in supporting Treg differentiation. Importantly, it has been demonstrated that significant increases in CD3⁺CD4+CD25+FoxP3⁺ cells in the colons of germ-free mice and conventional mice colonized with R. hominis using both flow cytometry and immunocytochemistry. These findings complement the recent data on other Clostridium species that drive Treg differentiation. Clearly, R. hominis can as a single bacterial species promote mucosal T cell expansion and impact on T cell differentiation.

Flagellin signals are perceived by host TLR5 receptors and many pathogenic flagellin structures induce strong pro-inflammatory responses (Hayashi et al. 2001). Signalling through TLR5 in response to resident flagellated commensals may be important for homeostasis, since deletion of TLR5 results in spontaneous colitis in mice (Vijay-Kumar et al. 2007). The enhanced expression of R. hominis flagellin FlaA1 (RH1) in vivo and its potency in activating epithelial cells and BMDCs is of great interest. Other work has shown that E. coli flagellin mutants have a colonization advantage over wild-type flagellated strains, possibly due to absence of innate recognition by TLR5 signalling (De Paepe et al. 2011, Giraud et al. 2008). Herein it is shown that for certain Firmicutes, the expression or possibly up-regulation of flagellin is a natural response to gut colonization. R. hominis flagellin protein remains expressed in vivo and correlates with sustained colonization, absence of overt inflammation and expansion of T cells of regulatory phenotype. The recent confirmation of flagellin genes in SFB (Prakash et al. 2011, Sczesnak et al. 2011) may correlate with the host T cell responses induced by this bacterium (Gaboriau-Routhiau et al. 2009, Ivanov et al. 2009). Interestingly, RH1 induced a unique effect on both epithelial and DC cultures compared to other flagellins, although all tested structures possess the conserved Arg90 associated with flagellins that bind and activate TLR5 (Yoon et al. 2012) suggesting that other sequence/structural differences may account for the unique signalling responses mediated by RH1. The significance of flagellin-TLR5 signalling in Treg responses induced by R. hominis was confirmed using TLR5KO. Without wishing to be bound by theory, certain commensal flagellin structures may help to direct immune tolerance responses through TLR5 expressed on either CD103+DC or Treg subsets (Flores-Langarica et al. 2012, Kinnebrew et al. 2012, Crellin et al. 2005). Furthermore, the immune homeostatic effect of R. hominis was confirmed in DSS-treated mice, although other signalling moieties, such as butyrate, may also contribute to immune tolerance. This data suggests a potential therapeutic benefit of R. hominis in IBD.

An interesting additional biological effect of R. hominis colonization was the regulation of genes influencing responses to food and control of appetite. In particular, the satiety hormones Cck and Gcg were significantly reduced. The effects of Cck on food intake are mediated via a vagal afferent pathway. This is the major neural pathway by which information about ingested nutrients reaches the central nervous system to influence both gut function and feeding behaviour. Cck acts on the vagal system to decrease expression of molecules that stimulate appetite and feeding, and to increase expression of molecules that inhibit feeding and decrease appetite (Npy2r and Cartpt, both down-regulated two-fold in the current study). No link between Cck, Gcg and commensal bacteria has been reported thus far, however, both fatty acids and proteins are potent inducers of Cck and Gcg (Geraedts et al. 2010). R. hominis produces short-chain fatty acids such as butyrate with aliphatic tails of less than six carbons; this metabolic activity has been reported to reduce the stimulatory effect on plasma Cck observed with longer chain fatty acids (McLaughlin et al. 1999). Carcass weight analysis revealed that both body weight and lipid content was indeed significantly increased with R. hominis, consistent with body weight increases observed in conventionalization of germfree mice (Turnbaugh et al. 2006). Whether this is a direct effect of a reduction in satiety hormones as seen in the current study remains to be seen, as the involvement of Cck and Gcg has not been reported previously. However, it is important to acknowledge that a link between microbiota colonization and energy harvest from the diet, in part through release of SCFAs, has been shown previously (Turnbaugh et al. 2006) (Tremaroli, Kovatcheva-Datchary & Backhed 2010). Given that R. hominis is a major butyrate producer, this mechanism is likely also to contribute to the metabolic efficiency observed following R. hominis treatment.

In summary, mono-association of the murine gut with R. hominis induced strong bi-directional gene expression events culminating in commensal bacterial adaptation and host tolerance. The flagellin product RH1 seems to exert a unique signaling effect, which preferentially drives expansion of Tregs. The importance of TLR5 in directing Treg differentiation and expansion has been demonstrated. Collectively, this data highlights additional functionality of commensal flagellins, TLR5 signaling and the net direction of the mucosal T cell response.

Functional Assays In Vitro Model Analysis of the Response of Intestinal Epithelial Cells (IECs) to Different Recombinant Flagellins.

Molecular analysis of CCL20 gene expression (a pro-inflammatory gene) after stimulation of IECs to different recombinant flagellins (FIG. 23) pathogenic flagellins (SE, ST, LF, and HM) induced similar but not identical levels of CCL20 mRNA, commensal flagellins displayed much more variable levels of induction. ER (Eubacterium rectale 33656), K12 (Escherichia coli K12), RH1 and RI3 flagellins induced CCL20 at similar levels to pathogenic flagellins, RI1 and RI4 had intermediate stimulatory activity, RH2 revealed as a low inducer of CCL20 in HT-29 and was devoid of agonistic potential in Caco-2 cells, and RI2 had no observable activity in both cell lines. In conclusion, the inventors distinguished three categories of TLR5 agonists (i) those with no or very low immunostimulatory activity, (ii) those with intermediate immunostimulatory activity and (iii) those with high immunostimulatory activity.

TABLE-US-00031 Table D2.

** ** ** *** * NS ** * * *

* ** NS NS NS * NS * NS *

** NS * NS * ** NS * NS **

** NS NS NS NS * NS * NS *

** NS NS NS * *** * ** NS *** {close oversize brace} HT-29 Caco-2 {open oversize brace}

*** NS * ** * NS ** NS * NS

NS NS ** ** ** *** ** * * *

** NS ** ** ** NS ** ** NS **

* NS ** ** ** * NS *** NS *

* NS NS NS ** NS * NS * *

NS NS ** ** ** ** NS ** NS * Table D2 indicates significant differences between each treatment calculated with paired t test in HT-29 (upper right) and Caco-2 (lower left). T tests used were unilateral to compare treatments to unstimulated cells (unstim) and bilateral to compare one treatment with another. NS (non significant); * (p < 0.05); ** (p < 0.01); *** (p < 0.001).

indicates data missing or illegible when filed

Cellular and immunological analysis of the effects of the recombinant flagellins on the IECs was determined by measurement of cytokines, CXCL8, CXCL10 and CCL2 (MCP-1) secreted. IECS were stimulated for 24 hrs with recombinant flagellins (FIG. 24).

The flagellins ST, SE, K12, ER, RI3 and RH1 induced the secretion of variable but similar levels of IL-8, IP-10 and MCP-1 chemokines, while RI1, RI2, RI4 and RH2, especially in Caco-2 behaved as low agonists of TLR5, inducing significantly lower amounts of secreted chemokines.

TABLE-US-00033 Table D3b

indicates data missing or illegible when filed

TABLE-US-00032 Table D3a

indicates data missing or illegible when filed

TABLE-US-00035 Table D3d

indicates data missing or illegible when filed

TABLE-US-00034 Table D3c

indicates data missing or illegible when filed

Tables D3a, D3b, D3c and D3d indicate significant differences between each treatment calculated with paired t test. The upper right side of Table D3a and D3b give t values for IL-8 and the lower left side for IP-10, and Tables D3c and D3d give t values for MCP-1. NS (non significant); *(p<0.05); ** (p<0.01); *** (p<0.001).

As shown in FIG. 25, neutralization of TLR5 with an anti-TLR5 specific antibody abolished the flagellin-mediated inflammatory response, independent of the commensal or pathogenic origin of flagellin. Therefore, the pro-inflammatory effects of flagellin observed in Caco-2 cells are dependent on TLR5 activation.

Generation of Bone Marrow-Derived Dendritic Cells and Cultures

Bone marrow was harvested from femur and tibia of C3H/HeN and C57B16 mice. For GMCSF-derived dendritic cells, bone marrow cells were resuspended at 1×10⁶/mL in RPMI supplemented with 10% FCS and 20 ng/mL rmGM-CSF and seeded at 10 mL/plate in 100 mm² tissue culture plates. After three days culture, loosely adherent cells were collected and replated with GM-CSF supplemented media at 1×10⁶/mL in 12 well tissue culture plates. At day 5, cells were stimulated with 100 ng/mL flagellins before being harvested on day 6. For Flt3L-derived dendritic cells, bone marrow cells were resuspended at 2×10⁶/mL in RPMI supplemented with 10% FCS and 200 ng/mL rmFlt3 and seeded at 2 mL/well in 12-well tissue culture plates. Cells were cultured for 10 days with Flt3 supplemented media added to each well on day 4. At day 9, cells were stimulated with 100 ng/mL flagellins before being harvested on day 10 and analyzed by flow cytometry.

Flow Cytometry Analysis of GM-CSF/IL-4 derived dendritic cells (FIG. 26) and Flt3L derived dendritic cells (FIG. 27) stimulated with recombinant flagellins was carried out. Flagellin Rh1 was most potent at inducing cellular response in GM-CSF/IL-4 derived dendritic cells with Ri4 and Ri3 having a similar response to commensal flagellins K12 and Er and pathogenic flagellins SE and ST. In contrast Rh2, and Ri2 did not induce cellular response with the GM-CSF/IL-4 derived dendritic cells but significantly increase cellular responses to Flt3L derived dendritic cells. These flagellins and in particular Ri1, are distinctive in their ability to elicit difference in responses with the activation of Flt3L-derived dendritic cells. This response signifies the specificity of the flagellins to a specific subset of dendritic cells. These Flt3L derived dendritic cells are categorised as plasmocytoid dendritic cells which play an important role in immunological tolerance.

In Vivo Model

BOY/J WT and TLRSKO mice were used to evaluate the functional importance of R. hominis and its flagellins. The mice were colonised with R. hominis. The animals were euthanized and intestinal tissue sampling was performed. Small intestine was collected for immunological analysis by flow cytometry.

Flow cytometry analysis of T cell populations, in particular, T regulatory (Treg) cells, in small intestine lamina propria was carried out (FIGS. 6 A and B). The percentage of FoxP3+CD25+ cells in CD4+ T cell population was significantly higher in the BOY/J WT mice in comparison to the TLR5KO mice. This indicates that R. hominis and more specifically the flagellins influences T regs by promoting CD4+ FoxP3+CD25+ regulatory T cells Therefore it can be concluded that flagellins are important in directing host immune response through TLR5 interactions.

Summary Clauses

The present invention is defined in the claims and the accompanying description. For convenience other aspects of the present invention are presented herein by way of numbered clauses.

1. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in regulating the immune system of a subject. 2. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, according to clause 1 for use in regulating the adaptive immune system of a subject. 3. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, according to clause 1 for use in regulating the innate immune system of a subject. 4. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in maintaining immune homeostasis in a subject. 5. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in treating an immune disorder in a subject. 6. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to clause 5, wherein the immune disorder is selected from ulcerative colitis, pouchitis, other autoimmune conditions including rheumatoid arthritis, psoriasis, multiple sclerosis, allergies including coeliac disease, atopic dermatitis and rhinitis. 7. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in treating a disorder selected from an inflammatory disorder, an immune disorder and an intestinal disorder in a subject. 8. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to clause 7, wherein the disorder is selected from irritable bowel syndrome (IBS), colitis, inflammatory bowel disorder (IBD), including Crohn's disease and ulcerative colitis, pouchitis, functional dyspepsia, functional constipation, functional diarrhoea (including antibiotic associated diarrhoea, traveller's diarrhoea and pediatric diarrhoea), functional abdominal pain, functional bloating, Epigastric Pain Syndrome, Postprandial Distress Syndrome, gastrointestinal reflux disease (GERD), autoimmune diseases such as diabetes, arthritis, multiple sclerosis and psoriasis allergies, atopic diseases e.g. atopic dermatitis, necrotising enterocolitis, other infections, and combinations thereof. 9. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in improving intestinal microbiota in a subject. 10. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in regulating appetite in a subject. 11. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in promoting gut health in a subject. 12. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in promoting Tregs cells and tolerance mechanisms in the immune system of a subject. 13. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any one of clauses 1 to 12, which regulates the induction and/or expression of at least one mobilization or chemotaxis gene. 14. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to clause 13, which upregulates the expression of at least one mobilization or chemotaxis gene, and wherein said gene is selected from MobA and MobL. 15. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause, which regulates at least one gene selected from FlaA1, Flat, FlaA3, and FlaB. 16. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause, which regulates the expression of at least one of the following: acetyl-CoA acetyltransferase, 3-hydroxyacyl-CoA dehydrogenase, butyryl-CoA dehydrogenase, electron transfer flavoprotein beta subunit, electron transfer flavoprotein alpha subunit. 17. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause, which downregulates the expression of at least one gene selected from Agt, Cartpt, Cck, Cxcl12 and Gcg. 18. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause, which activates at least one immune response gene in the colon or ileum. 19. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1 and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause, which activates the adaptive immune response by regulating the induction and/or expression of genes associated with T-cell regulation. 20. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause which upregulates expression of at least one gene selected from Ly6 g6c and Ly6 g6e in the ascending colon. 21. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1 and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, for use according to any preceding clause which regulates the expression of at least one gene selected from Tlr5, Tlr1, Vnn1, Defb37, Pla2 g, Muc16, ltln, Sprr1a, Cldn4, Pmp22, Crb3, Magi3, Marveld3, Mpp7, Defcr20, Pcgf2, Ltbp4, lgsf8 and Tcfe2a. 22. Use of Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, in the preparation of a medicament for regulating the immune system of a subject. 23. Use of Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, according to clause 22 in the preparation of a medicament for regulating the innate immune system of a subject. 24. Use of Roseburia (such as a bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or the polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, according to clause 22 in the preparation of a medicament for regulating the adaptive immune system of a subject. 25. Use of Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or a polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, in the preparation of a medicament for maintaining immune homeostasis in a subject. 26. Use of Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1 and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, in the preparation of a medicament for treating an immune disorder in a subject. 27. A method of regulating the immune system of a subject, said method comprising administering to the subject a composition comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 28. A method of activating the innate immune system of a subject, said method comprising administering to the subject a composition comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 29. A method of activating the adaptive immune system of a subject, said method comprising administering to the subject a composition comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1 and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 30. A method of treating an immune disorder in a subject, said method comprising administering to the subject a pharmaceutically effective amount of Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 31. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence for use according to any one of clauses 1 to 21, or a method according to any one of clauses 27 to 30, or a use according to any one of clauses 22 to 26, wherein the subject is a mammal. 32. Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, for use in medicine. 33. A pharmaceutical composition comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and a pharmaceutically acceptable excipient, carrier or diluent. 34. A nutritional supplement comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence, and a nutritionally acceptable excipient, carrier or diluent. 35. A probiotic composition comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 36. A feedstuff, food product, dietary supplement, nutritional supplement or food additive comprising Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or polypeptide FlaA1, and/or a polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or a vector comprising said polynucleotide sequence, and/or a host cell comprising said vector, and/or a host cell comprising said polynucleotide sequence. 37. A process for producing a pharmaceutical composition according to clause 32, said process comprising admixing Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, with a pharmaceutically acceptable excipient, carrier or diluent. 38. A process for producing a nutritional supplement according to clause 33, said process comprising admixing Roseburia (such as the bacterial species Roseburia hominis, or the bacterial species Roseburia intestinalis), and/or the polypeptide FlaA1, and/or the polynucleotide sequence encoding said polypeptide, and/or Roseburia flagellin, and/or a polynucleotide encoding said Roseburia flagellin, and/or the vector, and/or the host cell comprising said vector, and/or the host cell comprising said polynucleotide sequence, with a nutritionally acceptable excipient, carrier or diluent.

SUMMARY PARAGRAPHS

For convenience other aspects of the present invention are presented herein by way of numbered paragraphs.

1. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in modulating the inflammation of a tissue or an organ in a subject. 2. The polypeptide or the polynucleotide according to paragraph 1 wherein said polypeptide or polynucleotide reduces the inflammation of the tissue or the organ. 3. The polypeptide or the polynucleotide according to paragraph 2 wherein said polypeptide or polynucleotide reduces the inflammation by epithelial cells of the tissue or the organ. 4. The polypeptide or the polynucleotide according to paragraph 3 wherein said epithelial cells are epithelial cells of the alimentary canal. 5. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in modulating the production of T cells in a subject; preferably, the polypeptide or the polynucleotide increases the production of T regulatory cells in a subject. 6. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in restoring immunological tolerance. 7. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the immune system and restoring immunological tolerance of a subject. 8. The polypeptide or the polynucleotide according to paragraph 7 for use in regulating the adaptive immune system of a subject. 9. The polypeptide or the polynucleotide according to paragraph 7 for use in regulating the innate immune system of a subject. 10. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in treating a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder. 11. The polypeptide or the polynucleotide according to paragraph 10 wherein said disorder affects the alimentary canal or a section thereof of said subject. 12. The polypeptide or the polynucleotide according to paragraph 10 wherein said disorder is selected from the group consisting of rheumatoid arthritis, psoriasis, multiple sclerosis, type I diabetes, coeliac disease, atopic dermatitis, rhinitis, irritable bowel syndrome (IBS), colitis, inflammatory bowel disorder (IBD), ulcerative colitis, pouchitis, Crohn's disease, functional dyspepsia, atopic diseases, necrotising enterocolitis, and combinations thereof. 13. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in modulating dendritic cells and/or epithelial cells in a tissue or an organ of a subject. 14. The polypeptide or the polynucleotide according to paragraph 13 wherein said polypeptide or polynucleotide activates dendritic cells and/or epithelial cells. 15. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the production of IL-10 and/or TGF□ in a cell or cells of a subject. 16. The polypeptide or the polynucleotide according to paragraph 15 wherein the production of IL-10 is by dendritic cells. 17. The polypeptide or the polynucleotide according to paragraph 15 or 16 wherein said polypeptide or polynucleotide upregulates the production of IL-10 and/or TGF□. 18. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the production of CD40 and/or I-A/I-E in a cell or cells of a subject. 19. The polypeptide or the polynucleotide according to paragraph 18 wherein the production of CD40 and/or I-A/I-E is by dendritic cells. 20. The polypeptide or the polynucleotide according to paragraph 18 or 19 wherein said polypeptide or polynucleotide upregulates the production CD40 and/or I-A/I-E. 21. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the expression of one or more Type I IFN genes in a cell or cells of a subject. 22. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the expression of one or more pro-inflammatory genes in a cell or cells of a subject. 23. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in improving intestinal microbiota in a subject. 24. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating appetite in a subject. 25. The polypeptide or polynucleotide according to paragraph 24 wherein said polypeptide or polynucleotide stimulates the appetite in the subject. 26. The polypeptide or polynucleotide according to paragraph 24 or 25 wherein the level of cholecystokinin (Cck) and/or glucagon (Gcg) is reduced in the blood of a subject. 27. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in regulating the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject. 28. Polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for use in improving alimentary canal health in a subject. 29. The polypeptide or polynucleotide according to any one of paragraphs 1 to 28 wherein said polypeptide or polynucleotide is encapsulated. 30. A pharmaceutical composition comprising polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and a pharmaceutically acceptable excipient, carrier or diluent. 31. The pharmaceutical composition according to paragraph 30 wherein said polypeptide or polynucleotide is encapsulated. 32. A nutritional supplement comprising polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and a nutritional acceptable excipient, carrier or diluent. 33. The nutritional supplement according to paragraph 32 wherein said polypeptide or polynucleotide is encapsulated. 34. A feedstuff, food product, dietary supplement, or food additive comprising polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide. 35. The feedstuff, food product, dietary supplement, or food additive according to paragraph 34 wherein said feedstuff, food product, dietary supplement, or food additive is encapsulated. 36. A process for producing a pharmaceutical composition according to paragraph 30, said process comprising admixing said polypeptide or polynucleotide with a pharmaceutically acceptable excipient, carrier or diluent; optionally said polypeptide or polynucleotide is encapsulated. 37. A process for producing a nutritional supplement according to paragraph 32, said process comprising admixing said polypeptide or polynucleotide with a nutritionally acceptable excipient, carrier or diluent; optionally said polypeptide or polynucleotide is encapsulated. 38. A method of modulating the inflammation of a tissue or an organ in a subject, said method comprising administering to the subject polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, and wherein the inflammation of the tissue or organ in the subject is modulated. 39. A method of modulating the production of T cells in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, and wherein the production of T cells in the subject is modulated, in particular T regulatory cells. 40. A method of regulating the immune system of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, and wherein the immune system of the subject is regulated. 41. A method of treating a disorder in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder. 42. A method of modulating dendritic cells and/or epithelial cells in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, and wherein dendritic cells and/or epithelial cells in the subject are modulated. 43. A method of regulating the production of IL-10 and/or TGF□ in a cell or cells of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide to the subject, and wherein the production of IL-10 and/or TGF□ in a cell or cells of the subject is regulated. 44. A method of regulating the production of CD40 and/or I-A/I-E in a cell or cells of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide to the subject, and wherein the production of CD40 and/or I-A/I-E in a cell or cells of the subject is regulated. 45. A method of regulating the expression of one of more Type I IFN genes in a cell or cells of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide wherein the expression of one of more Type I IFN genes in a cell or cells of the subject is regulated. 46. A method of regulating the expression of one or more pro-inflammatory genes in a cell or cells of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, wherein the expression of one or more pro-inflammatory genes in a cell or cells of the subject is regulated. 47. A method of improving intestinal microbiota in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and wherein the intestinal microbiota in a subject is improved. 48. A method of regulating appetite in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and wherein the appetite in the subject is regulated. 49. A method of regulating the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and wherein the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of the subject is regulated. 50. A method of improving alimentary canal health in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide, and wherein alimentary canal health in a subject is improved. 51. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for modulating the inflammation of a tissue or an organ in a subject. 52. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for modulating the production of T cells in a subject. 53. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the immune system of a subject. 54. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for the treatment of a disorder in a subject, wherein said disorder is an inflammatory disorder and/or an autoimmune disorder. 55. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for modulating dendritic cells and/or epithelial cells in a tissue or an organ of a subject. 56. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the production of IL-10 and/or TGF□ in a cell or cells of a subject. 57. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the production of CD40 and/or I-A/I-E in a cell or cells of a subject. 58. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the expression of one of more Type I IFN genes in a cell or cells of a subject. 59. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the expression of one or more pro-inflammatory genes in a cell or cells of a subject. 60. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for improving intestinal microbiota in a subject. 61. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating appetite in a subject. 62. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for regulating the expression of the gene encoding cholecystokinin (Cck) and/or the expression of the gene encoding glucagon (Gcg) in a cell or cells of a subject. 63. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for improving alimentary canal health in a subject. 64. Use of polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide for the manufacture of a medicament for restoring immunological tolerance in a subject. 65. A method of restoring immunological tolerance in a subject, said method comprising administering polypeptide FlaA1 or a polynucleotide sequence encoding said polypeptide and wherein the immunological tolerance in a subject is restored.

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REFERENCE LIST FOR SUPPLEMENTARY INFORMATION

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1-68. (canceled)
 69. A method of reducing inflammation in a subject in need thereof, comprising administering to the subject of a pharmaceutical composition that comprises an amount of a Roseburia flagellin polypeptide sufficient to increase a level of IL-10 in the subject, relative to a level of IL-10 prior to the administering, thereby reducing inflammation.
 70. The method of claim 69, wherein the Roseburia flagellin comprises a polypeptide sequence having at least 75% identity to the polypeptide sequence of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 71. The method of claim 70, wherein the polypeptide sequence comprises a region that has at least 75% identity to amino acids 79-117 of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 72. The method of claim 69, wherein the Roseburia flagellin comprises a polypeptide sequence having at least 80% identity to the polypeptide sequence of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 73. The method of claim 72 wherein the polypeptide sequence comprises a region that has at least 80% identity to amino acids 79-117 of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 74. The method of claim 69, wherein the Roseburia flagellin polypeptide comprises a polypeptide sequence having at least 85% identity to the polypeptide sequence of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 75. The method of claim 74 wherein the polypeptide sequence comprises a region that has at least 85% identity to amino acids 79-117 of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 76. The method of claim 69, wherein the Roseburia flagellin polypeptide has at least 99% identity to the polypeptide sequence of SEQ ID NO: 2, as determined by a sequence alignment performed using BLAST.
 77. The method of claim 69, wherein the Roseburia flagellin polypeptide has a polypeptide sequence of SEQ ID NO:
 2. 78. The method of claim 69, wherein the Roseburia flagellin polypeptide binds to TLR5.
 79. The method of claim 69, wherein the Roseburia flagellin polypeptide is a FlaA1 polypeptide.
 80. The method of claim 69, wherein the Roseburia flagellin polypeptide comprises a Roseburia hominis flagellin polypeptide or a Roseburia intestinalis flagellin polypeptide.
 81. The method of claim 69, wherein the pharmaceutical composition is an enteric formulation.
 82. The method of claim 69, wherein the administering is oral.
 83. The method of claim 69, wherein the administering is rectal.
 84. The method of claim 69, wherein the Roseburia flagellin polypeptide is comprised in a fusion protein.
 85. The method of claim 69, wherein the pharmaceutical composition is a solid composition.
 86. The method of claim 69, wherein the pharmaceutical composition is in the form of one or more tablets or capsules.
 87. A method of modulating production of T cells in a subject, comprising administering to the subject a pharmaceutical composition comprising an amount of a Roseburia flagellin polypeptide sufficient to modulate the production of T cells in the subject.
 88. A method of regulating an immune system of a subject, said method comprising administering a pharmaceutical composition comprising an amount of a Roseburia flagellin polypeptide sufficient to regulate the immune system of the subject. 